diff --git a/.Rbuildignore b/.Rbuildignore
index 62652f5..18eae90 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1 +1,3 @@
-^\.github$
\ No newline at end of file
+^\.github$
+^_pkgdown\.yml$
+^CITATION\.cff$
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 93585ca..2133e3b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,49 +1,20 @@
-name: pkgdown
+name: PR CMD check & build site
 
 on:
+  pull_request:
   push:
-    branches:
-      - devel
-      - 'RELEASE_*'
     paths:
       - 'DESCRIPTION'
       - '**.yml'
-      - 'vignettes/**'
-      - 'man/**'
-
-permissions:
-  contents: write
-  pages: write
-  id-token: write
+    branches:
+      - devel
+      - 'RELEASE_*'
 
 jobs:
-  pkgdown:
-    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "pkgdown"))
-          remotes::install_local(dependencies = TRUE)
-        shell: Rscript {0}
-
-      - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
-        shell: Rscript {0}
-
-      - name: Deploy to GitHub pages 🚀
-        if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4
-        with:
-          clean: false
-          branch: gh-pages
-          folder: docs
\ No newline at end of file
+  ci:
+    uses: waldronlab/.github/.github/workflows/bioc-pr-cmdcheck-pkgdown.yml@devel
+    secrets: inherit
+    permissions:
+      contents: write
+      pages: write
+      id-token: write
diff --git a/DESCRIPTION b/DESCRIPTION
index 949fff8..566b65b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: curatedCRCData
 Type: Package
 Title: Colorectal Cancer Gene Expression Analysis
-Version: 2.45.2
-Date: 2026-04-10
+Version: 2.45.3
+Date: 2026-10-03
 Authors@R: c(
     person("Princy", "Parsana", role = "aut"),
     person("Markus", "Riester", role = "aut"),
@@ -10,15 +10,22 @@ Authors@R: c(
     person("Levi", "Waldron", email = "lwaldron.research@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2725-0694")),
     person("National Cancer Institute", role = "fnd", comment = "5U24CA180996")
   )
-Description: The curatedCRC package provides relevant functions and data for gene expression analysis in patients with colorectal cancer.
+Description: Manually curated human colorectal cancer ExpressionSet objects
+    from 34 studies, with uniformly processed expression data and
+    standardized clinical metadata including survival outcomes. Datasets
+    are hosted on Zenodo and downloaded on first use, then cached locally
+    with BiocFileCache. Includes a configurable script for rule-based
+    creation of filtered dataset lists for meta-analysis.
 Depends: 
-    R (>= 4.0.0),
+    R (>= 4.6.0),
     Biobase
 Imports: 
-    BiocGenerics
+    BiocFileCache,
+    tools,
+    utils
 Suggests: 
     survival,
-    RUnit,
+    testthat (>= 3.0.0),
     metafor,
     genefilter,
     logging,
@@ -30,10 +37,11 @@ Suggests:
     rmarkdown
 VignetteBuilder: knitr
 License: Artistic-2.0
-Namespace: auto
 biocViews: 
     ExperimentData,
     CancerData,
     ExpressionData
 URL: https://github.com/waldronlab/curatedCRCData
 BugReports: https://github.com/waldronlab/curatedCRCData/issues
+BuildResaveData: no
+Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
index b6c9445..2ce1178 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,11 +1,5 @@
-# Default NAMESPACE created by R
-# Remove the previous line if you edit this file
-
-# Export all names
-exportPattern(".")
-
-# Import all packages listed as Imports or Depends
-import(
-  Biobase,
-  BiocGenerics
-)
\ No newline at end of file
+export(curatedCRCData)
+import(Biobase)
+importFrom(BiocFileCache, BiocFileCache, bfcrpath, bfcquery, bfcremove)
+importFrom(utils, read.csv)
+importFrom(tools, md5sum, R_user_dir)
diff --git a/NEWS.md b/NEWS.md
index 35b1777..bf00827 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,36 @@
+# curatedCRCData 2.46.0
+
+## SIGNIFICANT USER-VISIBLE CHANGES
+
+* The 34 datasets are no longer stored inside the package: they are hosted
+  on Zenodo and downloaded individually on first use, then cached locally
+  with `BiocFileCache`. This shrinks the installed package from ~400 MB to
+  a few MB.
+* New exported function `curatedCRCData()`: call it with no arguments to
+  list available datasets, with one dataset name to get an `ExpressionSet`,
+  or with several names to get a named list. `test = TRUE` loads small
+  offline subsets bundled with the package (used by examples, tests, and
+  the vignette).
+* Legacy `data(GSE39582_eset)` access still works (it downloads through the
+  same cache, deferred until the object is first used) but is deprecated
+  and will be removed in a future release.
+* `inst/extdata/createEsetList.R` now loads datasets through the getter; a
+  new `test.mode` option in the patientselection config files selects the
+  offline subsets.
+* The cache is package-specific (`tools::R_user_dir("curatedCRCData",
+  "cache")`); delete that directory to reclaim disk space. Downloads are
+  verified against md5 checksums recorded in
+  `inst/extdata/zenodo-manifest.csv`.
+
+## INTERNAL
+
+* Replaced the never-executed RUnit scaffolding with testthat tests.
+* CI restored to R CMD check + BiocCheck + pkgdown via the waldronlab
+  reusable workflow (previously reduced to pkgdown-only because checking
+  400 MB of data exhausted runner memory).
+* Removed `external_data_store.txt` and `Namespace: auto`; explicit
+  NAMESPACE exporting only `curatedCRCData()`.
+
 # curatedCRCData 2.43.1
 
 * Updated package maintainer to Levi Waldron (<lwaldron.research@gmail.com>).
diff --git a/R/getData.R b/R/getData.R
new file mode 100644
index 0000000..ad8bd32
--- /dev/null
+++ b/R/getData.R
@@ -0,0 +1,103 @@
+## Data retrieval for curatedCRCData: datasets are hosted on Zenodo and
+## downloaded on first use into a package-specific BiocFileCache.
+##
+## NOTE: this file is intentionally duplicated (modulo package name) in
+## curatedOvarianData. Keep the two copies in sync.
+
+.pkgname <- "curatedCRCData"
+
+## session flags (e.g., show the data() deprecation note only once)
+.pkgenv <- new.env(parent = emptyenv())
+
+## Manifest mapping dataset names to Zenodo file URLs, md5 checksums, and
+## sizes. Regenerated by inst/scripts/make-data.R; the manifest is the ONLY
+## place download URLs live.
+.manifest <- function() {
+    fname <- system.file("extdata", "zenodo-manifest.csv",
+                         package = .pkgname, mustWork = TRUE)
+    utils::read.csv(fname, stringsAsFactors = FALSE)
+}
+
+.cache <- function() {
+    BiocFileCache::BiocFileCache(tools::R_user_dir(.pkgname, "cache"))
+}
+
+## Return the local path to one dataset's .rda, downloading into the cache
+## on first use. The md5 checksum is verified after a fresh download only;
+## on mismatch the corrupt entry is removed and the download retried once.
+.getDataFile <- function(name, retry = TRUE) {
+    meta <- .manifest()
+    i <- match(name, meta$dataset)
+    stopifnot(!is.na(i))
+    bfc <- .cache()
+    known <- BiocFileCache::bfcquery(bfc, meta$url[i], field = "fpath",
+                                     exact = TRUE)
+    fresh <- nrow(known) == 0L
+    if (fresh)
+        message("Downloading ", name, " (",
+                round(meta$size_bytes[i] / 2^20, 1), " MB) from Zenodo...")
+    path <- unname(BiocFileCache::bfcrpath(bfc, meta$url[i]))
+    if (fresh) {
+        md5 <- unname(tools::md5sum(path))
+        if (!identical(md5, meta$md5[i])) {
+            res <- BiocFileCache::bfcquery(bfc, meta$url[i], field = "fpath",
+                                           exact = TRUE)
+            if (nrow(res))
+                BiocFileCache::bfcremove(bfc, res$rid)
+            if (retry) {
+                message("Checksum mismatch; retrying the download once...")
+                return(.getDataFile(name, retry = FALSE))
+            }
+            stop("md5 checksum mismatch for '", name, "' downloaded from ",
+                 meta$url[i],
+                 "; the corrupt copy was removed from the cache.")
+        }
+    }
+    path
+}
+
+.loadOne <- function(name, test = FALSE) {
+    path <- if (test) {
+        system.file("extdata", "testdata", paste0(name, ".rda"),
+                    package = .pkgname, mustWork = TRUE)
+    } else {
+        .getDataFile(name)
+    }
+    env <- new.env(parent = emptyenv())
+    objname <- load(path, envir = env)
+    get(objname[1L], envir = env)
+}
+
+## Called by the data/*.R stubs so that legacy data(X) usage keeps working.
+## During this package's own R CMD check, resolve to the bundled test
+## fixture so checking needs no network access; checks of OTHER packages
+## (reverse dependencies) get the real data.
+.stubLoad <- function(name) {
+    if (identical(Sys.getenv("_R_CHECK_PACKAGE_NAME_"), .pkgname))
+        return(.loadOne(name, test = TRUE))
+    if (!isTRUE(.pkgenv$stub_noted)) {
+        .pkgenv$stub_noted <- TRUE
+        message("Note: loading ", .pkgname, " datasets via data() is ",
+                "deprecated and will be removed in a future release; use ",
+                .pkgname, "(\"", name, "\") instead. Datasets are now ",
+                "downloaded on first use and cached locally with ",
+                "BiocFileCache. (This note is shown once per session.)")
+    }
+    .loadOne(name)
+}
+
+#' @export
+curatedCRCData <- function(datasets, test = FALSE) {
+    meta <- .manifest()
+    if (missing(datasets))
+        return(meta$dataset)
+    stopifnot(is.character(datasets), !anyNA(datasets))
+    bad <- setdiff(datasets, meta$dataset)
+    if (length(bad))
+        stop("Unknown dataset(s): ", paste(bad, collapse = ", "),
+             ". Call curatedCRCData() with no arguments to list ",
+             "available datasets.")
+    res <- lapply(datasets, .loadOne, test = test)
+    names(res) <- datasets
+    if (length(res) == 1L) res[[1L]] else res
+}
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..23958f9
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,7 @@
+title: curatedCRCData
+url: https://waldronlab.github.io/curatedCRCData
+
+template:
+  bootstrap: 5
+  params:
+    bootswatch: flatly
diff --git a/data/GSE11237_eset.R b/data/GSE11237_eset.R
new file mode 100644
index 0000000..909ee81
--- /dev/null
+++ b/data/GSE11237_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE11237_eset",
+    curatedCRCData:::.stubLoad("GSE11237_eset"),
+    assign.env = environment())
diff --git a/data/GSE11237_eset.rda b/data/GSE11237_eset.rda
deleted file mode 100644
index a204061..0000000
Binary files a/data/GSE11237_eset.rda and /dev/null differ
diff --git a/data/GSE12225.GPL3676_eset.R b/data/GSE12225.GPL3676_eset.R
new file mode 100644
index 0000000..a447f06
--- /dev/null
+++ b/data/GSE12225.GPL3676_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE12225.GPL3676_eset",
+    curatedCRCData:::.stubLoad("GSE12225.GPL3676_eset"),
+    assign.env = environment())
diff --git a/data/GSE12225.GPL3676_eset.rda b/data/GSE12225.GPL3676_eset.rda
deleted file mode 100644
index d8f6211..0000000
Binary files a/data/GSE12225.GPL3676_eset.rda and /dev/null differ
diff --git a/data/GSE12945_eset.R b/data/GSE12945_eset.R
new file mode 100644
index 0000000..8d49ecf
--- /dev/null
+++ b/data/GSE12945_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE12945_eset",
+    curatedCRCData:::.stubLoad("GSE12945_eset"),
+    assign.env = environment())
diff --git a/data/GSE12945_eset.rda b/data/GSE12945_eset.rda
deleted file mode 100644
index 8b80d5e..0000000
Binary files a/data/GSE12945_eset.rda and /dev/null differ
diff --git a/data/GSE13067_eset.R b/data/GSE13067_eset.R
new file mode 100644
index 0000000..3c11693
--- /dev/null
+++ b/data/GSE13067_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE13067_eset",
+    curatedCRCData:::.stubLoad("GSE13067_eset"),
+    assign.env = environment())
diff --git a/data/GSE13067_eset.rda b/data/GSE13067_eset.rda
deleted file mode 100644
index f23429c..0000000
Binary files a/data/GSE13067_eset.rda and /dev/null differ
diff --git a/data/GSE13294_eset.R b/data/GSE13294_eset.R
new file mode 100644
index 0000000..445ede9
--- /dev/null
+++ b/data/GSE13294_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE13294_eset",
+    curatedCRCData:::.stubLoad("GSE13294_eset"),
+    assign.env = environment())
diff --git a/data/GSE13294_eset.rda b/data/GSE13294_eset.rda
deleted file mode 100644
index 94214b9..0000000
Binary files a/data/GSE13294_eset.rda and /dev/null differ
diff --git a/data/GSE14095_eset.R b/data/GSE14095_eset.R
new file mode 100644
index 0000000..fdc8f5d
--- /dev/null
+++ b/data/GSE14095_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE14095_eset",
+    curatedCRCData:::.stubLoad("GSE14095_eset"),
+    assign.env = environment())
diff --git a/data/GSE14095_eset.rda b/data/GSE14095_eset.rda
deleted file mode 100644
index 739ba73..0000000
Binary files a/data/GSE14095_eset.rda and /dev/null differ
diff --git a/data/GSE14333_eset.R b/data/GSE14333_eset.R
new file mode 100644
index 0000000..b4c5605
--- /dev/null
+++ b/data/GSE14333_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE14333_eset",
+    curatedCRCData:::.stubLoad("GSE14333_eset"),
+    assign.env = environment())
diff --git a/data/GSE14333_eset.rda b/data/GSE14333_eset.rda
deleted file mode 100644
index d4f3404..0000000
Binary files a/data/GSE14333_eset.rda and /dev/null differ
diff --git a/data/GSE16125.GPL5175_eset.R b/data/GSE16125.GPL5175_eset.R
new file mode 100644
index 0000000..7dbd626
--- /dev/null
+++ b/data/GSE16125.GPL5175_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE16125.GPL5175_eset",
+    curatedCRCData:::.stubLoad("GSE16125.GPL5175_eset"),
+    assign.env = environment())
diff --git a/data/GSE16125.GPL5175_eset.rda b/data/GSE16125.GPL5175_eset.rda
deleted file mode 100644
index 5895b0c..0000000
Binary files a/data/GSE16125.GPL5175_eset.rda and /dev/null differ
diff --git a/data/GSE17536_eset.R b/data/GSE17536_eset.R
new file mode 100644
index 0000000..4fa34cc
--- /dev/null
+++ b/data/GSE17536_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE17536_eset",
+    curatedCRCData:::.stubLoad("GSE17536_eset"),
+    assign.env = environment())
diff --git a/data/GSE17536_eset.rda b/data/GSE17536_eset.rda
deleted file mode 100644
index c15e547..0000000
Binary files a/data/GSE17536_eset.rda and /dev/null differ
diff --git a/data/GSE17537_eset.R b/data/GSE17537_eset.R
new file mode 100644
index 0000000..aeacd9f
--- /dev/null
+++ b/data/GSE17537_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE17537_eset",
+    curatedCRCData:::.stubLoad("GSE17537_eset"),
+    assign.env = environment())
diff --git a/data/GSE17537_eset.rda b/data/GSE17537_eset.rda
deleted file mode 100644
index a6f67fa..0000000
Binary files a/data/GSE17537_eset.rda and /dev/null differ
diff --git a/data/GSE17538.GPL570_eset.R b/data/GSE17538.GPL570_eset.R
new file mode 100644
index 0000000..77426be
--- /dev/null
+++ b/data/GSE17538.GPL570_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE17538.GPL570_eset",
+    curatedCRCData:::.stubLoad("GSE17538.GPL570_eset"),
+    assign.env = environment())
diff --git a/data/GSE17538.GPL570_eset.rda b/data/GSE17538.GPL570_eset.rda
deleted file mode 100644
index b0c2cb0..0000000
Binary files a/data/GSE17538.GPL570_eset.rda and /dev/null differ
diff --git a/data/GSE18105_eset.R b/data/GSE18105_eset.R
new file mode 100644
index 0000000..29268be
--- /dev/null
+++ b/data/GSE18105_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE18105_eset",
+    curatedCRCData:::.stubLoad("GSE18105_eset"),
+    assign.env = environment())
diff --git a/data/GSE18105_eset.rda b/data/GSE18105_eset.rda
deleted file mode 100644
index dee4c2a..0000000
Binary files a/data/GSE18105_eset.rda and /dev/null differ
diff --git a/data/GSE2109_eset.R b/data/GSE2109_eset.R
new file mode 100644
index 0000000..fb51c6d
--- /dev/null
+++ b/data/GSE2109_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE2109_eset",
+    curatedCRCData:::.stubLoad("GSE2109_eset"),
+    assign.env = environment())
diff --git a/data/GSE2109_eset.rda b/data/GSE2109_eset.rda
deleted file mode 100644
index be33a31..0000000
Binary files a/data/GSE2109_eset.rda and /dev/null differ
diff --git a/data/GSE21510_eset.R b/data/GSE21510_eset.R
new file mode 100644
index 0000000..665978b
--- /dev/null
+++ b/data/GSE21510_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE21510_eset",
+    curatedCRCData:::.stubLoad("GSE21510_eset"),
+    assign.env = environment())
diff --git a/data/GSE21510_eset.rda b/data/GSE21510_eset.rda
deleted file mode 100644
index bfa9484..0000000
Binary files a/data/GSE21510_eset.rda and /dev/null differ
diff --git a/data/GSE21815_eset.R b/data/GSE21815_eset.R
new file mode 100644
index 0000000..6865313
--- /dev/null
+++ b/data/GSE21815_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE21815_eset",
+    curatedCRCData:::.stubLoad("GSE21815_eset"),
+    assign.env = environment())
diff --git a/data/GSE21815_eset.rda b/data/GSE21815_eset.rda
deleted file mode 100644
index d5e8266..0000000
Binary files a/data/GSE21815_eset.rda and /dev/null differ
diff --git a/data/GSE24549.GPL5175_eset.R b/data/GSE24549.GPL5175_eset.R
new file mode 100644
index 0000000..cc6d12d
--- /dev/null
+++ b/data/GSE24549.GPL5175_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE24549.GPL5175_eset",
+    curatedCRCData:::.stubLoad("GSE24549.GPL5175_eset"),
+    assign.env = environment())
diff --git a/data/GSE24549.GPL5175_eset.rda b/data/GSE24549.GPL5175_eset.rda
deleted file mode 100644
index 3e1363c..0000000
Binary files a/data/GSE24549.GPL5175_eset.rda and /dev/null differ
diff --git a/data/GSE24550.GPL5175_eset.R b/data/GSE24550.GPL5175_eset.R
new file mode 100644
index 0000000..8ae7abf
--- /dev/null
+++ b/data/GSE24550.GPL5175_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE24550.GPL5175_eset",
+    curatedCRCData:::.stubLoad("GSE24550.GPL5175_eset"),
+    assign.env = environment())
diff --git a/data/GSE24550.GPL5175_eset.rda b/data/GSE24550.GPL5175_eset.rda
deleted file mode 100644
index b00ae22..0000000
Binary files a/data/GSE24550.GPL5175_eset.rda and /dev/null differ
diff --git a/data/GSE2630_eset.R b/data/GSE2630_eset.R
new file mode 100644
index 0000000..6907bed
--- /dev/null
+++ b/data/GSE2630_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE2630_eset",
+    curatedCRCData:::.stubLoad("GSE2630_eset"),
+    assign.env = environment())
diff --git a/data/GSE2630_eset.rda b/data/GSE2630_eset.rda
deleted file mode 100644
index 8730ed2..0000000
Binary files a/data/GSE2630_eset.rda and /dev/null differ
diff --git a/data/GSE26682.GPL570_eset.R b/data/GSE26682.GPL570_eset.R
new file mode 100644
index 0000000..e49d1df
--- /dev/null
+++ b/data/GSE26682.GPL570_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE26682.GPL570_eset",
+    curatedCRCData:::.stubLoad("GSE26682.GPL570_eset"),
+    assign.env = environment())
diff --git a/data/GSE26682.GPL570_eset.rda b/data/GSE26682.GPL570_eset.rda
deleted file mode 100644
index 68522b4..0000000
Binary files a/data/GSE26682.GPL570_eset.rda and /dev/null differ
diff --git a/data/GSE26682.GPL96_eset.R b/data/GSE26682.GPL96_eset.R
new file mode 100644
index 0000000..2b8b4f8
--- /dev/null
+++ b/data/GSE26682.GPL96_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE26682.GPL96_eset",
+    curatedCRCData:::.stubLoad("GSE26682.GPL96_eset"),
+    assign.env = environment())
diff --git a/data/GSE26682.GPL96_eset.rda b/data/GSE26682.GPL96_eset.rda
deleted file mode 100644
index a583637..0000000
Binary files a/data/GSE26682.GPL96_eset.rda and /dev/null differ
diff --git a/data/GSE26906_eset.R b/data/GSE26906_eset.R
new file mode 100644
index 0000000..d63f6ec
--- /dev/null
+++ b/data/GSE26906_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE26906_eset",
+    curatedCRCData:::.stubLoad("GSE26906_eset"),
+    assign.env = environment())
diff --git a/data/GSE26906_eset.rda b/data/GSE26906_eset.rda
deleted file mode 100644
index a28e22d..0000000
Binary files a/data/GSE26906_eset.rda and /dev/null differ
diff --git a/data/GSE27544_eset.R b/data/GSE27544_eset.R
new file mode 100644
index 0000000..44cb3b8
--- /dev/null
+++ b/data/GSE27544_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE27544_eset",
+    curatedCRCData:::.stubLoad("GSE27544_eset"),
+    assign.env = environment())
diff --git a/data/GSE27544_eset.rda b/data/GSE27544_eset.rda
deleted file mode 100644
index c48f4c6..0000000
Binary files a/data/GSE27544_eset.rda and /dev/null differ
diff --git a/data/GSE28702_eset.R b/data/GSE28702_eset.R
new file mode 100644
index 0000000..6700c58
--- /dev/null
+++ b/data/GSE28702_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE28702_eset",
+    curatedCRCData:::.stubLoad("GSE28702_eset"),
+    assign.env = environment())
diff --git a/data/GSE28702_eset.rda b/data/GSE28702_eset.rda
deleted file mode 100644
index f00108a..0000000
Binary files a/data/GSE28702_eset.rda and /dev/null differ
diff --git a/data/GSE3294_eset.R b/data/GSE3294_eset.R
new file mode 100644
index 0000000..ab4f8b2
--- /dev/null
+++ b/data/GSE3294_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE3294_eset",
+    curatedCRCData:::.stubLoad("GSE3294_eset"),
+    assign.env = environment())
diff --git a/data/GSE3294_eset.rda b/data/GSE3294_eset.rda
deleted file mode 100644
index feb4285..0000000
Binary files a/data/GSE3294_eset.rda and /dev/null differ
diff --git a/data/GSE33113_eset.R b/data/GSE33113_eset.R
new file mode 100644
index 0000000..c344051
--- /dev/null
+++ b/data/GSE33113_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE33113_eset",
+    curatedCRCData:::.stubLoad("GSE33113_eset"),
+    assign.env = environment())
diff --git a/data/GSE33113_eset.rda b/data/GSE33113_eset.rda
deleted file mode 100644
index 14b2121..0000000
Binary files a/data/GSE33113_eset.rda and /dev/null differ
diff --git a/data/GSE39582_eset.R b/data/GSE39582_eset.R
new file mode 100644
index 0000000..d4dee3a
--- /dev/null
+++ b/data/GSE39582_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE39582_eset",
+    curatedCRCData:::.stubLoad("GSE39582_eset"),
+    assign.env = environment())
diff --git a/data/GSE39582_eset.rda b/data/GSE39582_eset.rda
deleted file mode 100644
index 399b1af..0000000
Binary files a/data/GSE39582_eset.rda and /dev/null differ
diff --git a/data/GSE3964_eset.R b/data/GSE3964_eset.R
new file mode 100644
index 0000000..3530aa6
--- /dev/null
+++ b/data/GSE3964_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE3964_eset",
+    curatedCRCData:::.stubLoad("GSE3964_eset"),
+    assign.env = environment())
diff --git a/data/GSE3964_eset.rda b/data/GSE3964_eset.rda
deleted file mode 100644
index ae03eae..0000000
Binary files a/data/GSE3964_eset.rda and /dev/null differ
diff --git a/data/GSE4045_eset.R b/data/GSE4045_eset.R
new file mode 100644
index 0000000..59e7a77
--- /dev/null
+++ b/data/GSE4045_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE4045_eset",
+    curatedCRCData:::.stubLoad("GSE4045_eset"),
+    assign.env = environment())
diff --git a/data/GSE4045_eset.rda b/data/GSE4045_eset.rda
deleted file mode 100644
index e5c791f..0000000
Binary files a/data/GSE4045_eset.rda and /dev/null differ
diff --git a/data/GSE4526_eset.R b/data/GSE4526_eset.R
new file mode 100644
index 0000000..fe4e34d
--- /dev/null
+++ b/data/GSE4526_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE4526_eset",
+    curatedCRCData:::.stubLoad("GSE4526_eset"),
+    assign.env = environment())
diff --git a/data/GSE4526_eset.rda b/data/GSE4526_eset.rda
deleted file mode 100644
index f96b94f..0000000
Binary files a/data/GSE4526_eset.rda and /dev/null differ
diff --git a/data/GSE45270_eset.R b/data/GSE45270_eset.R
new file mode 100644
index 0000000..f7e8e20
--- /dev/null
+++ b/data/GSE45270_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("GSE45270_eset",
+    curatedCRCData:::.stubLoad("GSE45270_eset"),
+    assign.env = environment())
diff --git a/data/GSE45270_eset.rda b/data/GSE45270_eset.rda
deleted file mode 100644
index ead6cac..0000000
Binary files a/data/GSE45270_eset.rda and /dev/null differ
diff --git a/data/TCGA.COAD_eset.R b/data/TCGA.COAD_eset.R
new file mode 100644
index 0000000..01966ae
--- /dev/null
+++ b/data/TCGA.COAD_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("TCGA.COAD_eset",
+    curatedCRCData:::.stubLoad("TCGA.COAD_eset"),
+    assign.env = environment())
diff --git a/data/TCGA.COAD_eset.rda b/data/TCGA.COAD_eset.rda
deleted file mode 100644
index 9af1253..0000000
Binary files a/data/TCGA.COAD_eset.rda and /dev/null differ
diff --git a/data/TCGA.READ_eset.R b/data/TCGA.READ_eset.R
new file mode 100644
index 0000000..56c1441
--- /dev/null
+++ b/data/TCGA.READ_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("TCGA.READ_eset",
+    curatedCRCData:::.stubLoad("TCGA.READ_eset"),
+    assign.env = environment())
diff --git a/data/TCGA.READ_eset.rda b/data/TCGA.READ_eset.rda
deleted file mode 100644
index a7eb4b5..0000000
Binary files a/data/TCGA.READ_eset.rda and /dev/null differ
diff --git a/data/TCGA.RNASeqV2.READ_eset.R b/data/TCGA.RNASeqV2.READ_eset.R
new file mode 100644
index 0000000..79c833f
--- /dev/null
+++ b/data/TCGA.RNASeqV2.READ_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("TCGA.RNASeqV2.READ_eset",
+    curatedCRCData:::.stubLoad("TCGA.RNASeqV2.READ_eset"),
+    assign.env = environment())
diff --git a/data/TCGA.RNASeqV2.READ_eset.rda b/data/TCGA.RNASeqV2.READ_eset.rda
deleted file mode 100644
index 26d389e..0000000
Binary files a/data/TCGA.RNASeqV2.READ_eset.rda and /dev/null differ
diff --git a/data/TCGA.RNASeqV2_eset.R b/data/TCGA.RNASeqV2_eset.R
new file mode 100644
index 0000000..97a3a14
--- /dev/null
+++ b/data/TCGA.RNASeqV2_eset.R
@@ -0,0 +1,3 @@
+delayedAssign("TCGA.RNASeqV2_eset",
+    curatedCRCData:::.stubLoad("TCGA.RNASeqV2_eset"),
+    assign.env = environment())
diff --git a/data/TCGA.RNASeqV2_eset.rda b/data/TCGA.RNASeqV2_eset.rda
deleted file mode 100644
index 6305653..0000000
Binary files a/data/TCGA.RNASeqV2_eset.rda and /dev/null differ
diff --git a/data/datalist b/data/datalist
index 90bf526..0c8d987 100644
--- a/data/datalist
+++ b/data/datalist
@@ -30,5 +30,5 @@ GSE4526_eset
 GSE45270_eset
 TCGA.COAD_eset
 TCGA.READ_eset
-TCGA.RNASeqV2.READ_eset
 TCGA.RNASeqV2_eset
+TCGA.RNASeqV2.READ_eset
diff --git a/external_data_store.txt b/external_data_store.txt
deleted file mode 100644
index 0e0bceb..0000000
--- a/external_data_store.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-data
-inst/extdata
diff --git a/inst/extdata/createEsetList.R b/inst/extdata/createEsetList.R
index 6d0f0af..70d35b1 100644
--- a/inst/extdata/createEsetList.R
+++ b/inst/extdata/createEsetList.R
@@ -65,7 +65,10 @@ intersectMany <- function(lst){
 }
 
 ##load the esets
-data(list=data(package=package.name)[[3]][,3])
+if (!exists("test.mode")) test.mode <- FALSE
+for (.nm in do.call(package.name, list()))
+    assign(.nm, do.call(package.name, list(datasets = .nm, test = test.mode)))
+rm(.nm)
 
 strEsets <- ls(pattern="^.*_eset$")
 
@@ -145,8 +148,8 @@ if(keep.common.only){
     })
 }
 
-ids.with.missing.data <- which(sapply(esets, function(X)
-sum(!complete.cases(exprs(X))) > 0))
+ids.with.missing.data <- which(vapply(esets, function(X)
+sum(!complete.cases(exprs(X))) > 0, logical(1)))
 loginfo(paste("Ids with missing data:", paste(names(ids.with.missing.data),
 collapse=", ")))
 
diff --git a/inst/extdata/patientselection.config b/inst/extdata/patientselection.config
index 087ff2c..9085329 100644
--- a/inst/extdata/patientselection.config
+++ b/inst/extdata/patientselection.config
@@ -2,6 +2,10 @@
 ##settings for createEsetList.R
 ##-----------------------------
 
+#use the small offline test subsets bundled with the package instead of
+#downloading the full datasets from Zenodo? (for examples/vignettes/tests)
+test.mode <- FALSE
+
 #remove retracted studies?
 remove.retracted <- FALSE
 
diff --git a/inst/extdata/patientselection_all.config b/inst/extdata/patientselection_all.config
index fed7a06..c06460e 100755
--- a/inst/extdata/patientselection_all.config
+++ b/inst/extdata/patientselection_all.config
@@ -2,6 +2,10 @@
 ##settings for createEsetList.R
 ##-----------------------------
 
+#use the small offline test subsets bundled with the package instead of
+#downloading the full datasets from Zenodo? (for examples/vignettes/tests)
+test.mode <- FALSE
+
 #rescale each gene to z-score?
 rescale <- FALSE
 
diff --git a/inst/extdata/testdata/GSE11237_eset.rda b/inst/extdata/testdata/GSE11237_eset.rda
new file mode 100644
index 0000000..100a518
Binary files /dev/null and b/inst/extdata/testdata/GSE11237_eset.rda differ
diff --git a/inst/extdata/testdata/GSE12225.GPL3676_eset.rda b/inst/extdata/testdata/GSE12225.GPL3676_eset.rda
new file mode 100644
index 0000000..cebf165
Binary files /dev/null and b/inst/extdata/testdata/GSE12225.GPL3676_eset.rda differ
diff --git a/inst/extdata/testdata/GSE12945_eset.rda b/inst/extdata/testdata/GSE12945_eset.rda
new file mode 100644
index 0000000..ffeea06
Binary files /dev/null and b/inst/extdata/testdata/GSE12945_eset.rda differ
diff --git a/inst/extdata/testdata/GSE13067_eset.rda b/inst/extdata/testdata/GSE13067_eset.rda
new file mode 100644
index 0000000..0955086
Binary files /dev/null and b/inst/extdata/testdata/GSE13067_eset.rda differ
diff --git a/inst/extdata/testdata/GSE13294_eset.rda b/inst/extdata/testdata/GSE13294_eset.rda
new file mode 100644
index 0000000..50ebbca
Binary files /dev/null and b/inst/extdata/testdata/GSE13294_eset.rda differ
diff --git a/inst/extdata/testdata/GSE14095_eset.rda b/inst/extdata/testdata/GSE14095_eset.rda
new file mode 100644
index 0000000..c2a8604
Binary files /dev/null and b/inst/extdata/testdata/GSE14095_eset.rda differ
diff --git a/inst/extdata/testdata/GSE14333_eset.rda b/inst/extdata/testdata/GSE14333_eset.rda
new file mode 100644
index 0000000..e534792
Binary files /dev/null and b/inst/extdata/testdata/GSE14333_eset.rda differ
diff --git a/inst/extdata/testdata/GSE16125.GPL5175_eset.rda b/inst/extdata/testdata/GSE16125.GPL5175_eset.rda
new file mode 100644
index 0000000..8c8057f
Binary files /dev/null and b/inst/extdata/testdata/GSE16125.GPL5175_eset.rda differ
diff --git a/inst/extdata/testdata/GSE17536_eset.rda b/inst/extdata/testdata/GSE17536_eset.rda
new file mode 100644
index 0000000..0922bfb
Binary files /dev/null and b/inst/extdata/testdata/GSE17536_eset.rda differ
diff --git a/inst/extdata/testdata/GSE17537_eset.rda b/inst/extdata/testdata/GSE17537_eset.rda
new file mode 100644
index 0000000..96690db
Binary files /dev/null and b/inst/extdata/testdata/GSE17537_eset.rda differ
diff --git a/inst/extdata/testdata/GSE17538.GPL570_eset.rda b/inst/extdata/testdata/GSE17538.GPL570_eset.rda
new file mode 100644
index 0000000..52a7972
Binary files /dev/null and b/inst/extdata/testdata/GSE17538.GPL570_eset.rda differ
diff --git a/inst/extdata/testdata/GSE18105_eset.rda b/inst/extdata/testdata/GSE18105_eset.rda
new file mode 100644
index 0000000..13dce90
Binary files /dev/null and b/inst/extdata/testdata/GSE18105_eset.rda differ
diff --git a/inst/extdata/testdata/GSE2109_eset.rda b/inst/extdata/testdata/GSE2109_eset.rda
new file mode 100644
index 0000000..dd670bb
Binary files /dev/null and b/inst/extdata/testdata/GSE2109_eset.rda differ
diff --git a/inst/extdata/testdata/GSE21510_eset.rda b/inst/extdata/testdata/GSE21510_eset.rda
new file mode 100644
index 0000000..5e5532d
Binary files /dev/null and b/inst/extdata/testdata/GSE21510_eset.rda differ
diff --git a/inst/extdata/testdata/GSE21815_eset.rda b/inst/extdata/testdata/GSE21815_eset.rda
new file mode 100644
index 0000000..9647d2e
Binary files /dev/null and b/inst/extdata/testdata/GSE21815_eset.rda differ
diff --git a/inst/extdata/testdata/GSE24549.GPL5175_eset.rda b/inst/extdata/testdata/GSE24549.GPL5175_eset.rda
new file mode 100644
index 0000000..3a3e775
Binary files /dev/null and b/inst/extdata/testdata/GSE24549.GPL5175_eset.rda differ
diff --git a/inst/extdata/testdata/GSE24550.GPL5175_eset.rda b/inst/extdata/testdata/GSE24550.GPL5175_eset.rda
new file mode 100644
index 0000000..84e253b
Binary files /dev/null and b/inst/extdata/testdata/GSE24550.GPL5175_eset.rda differ
diff --git a/inst/extdata/testdata/GSE2630_eset.rda b/inst/extdata/testdata/GSE2630_eset.rda
new file mode 100644
index 0000000..d560b7d
Binary files /dev/null and b/inst/extdata/testdata/GSE2630_eset.rda differ
diff --git a/inst/extdata/testdata/GSE26682.GPL570_eset.rda b/inst/extdata/testdata/GSE26682.GPL570_eset.rda
new file mode 100644
index 0000000..ad16193
Binary files /dev/null and b/inst/extdata/testdata/GSE26682.GPL570_eset.rda differ
diff --git a/inst/extdata/testdata/GSE26682.GPL96_eset.rda b/inst/extdata/testdata/GSE26682.GPL96_eset.rda
new file mode 100644
index 0000000..32096b0
Binary files /dev/null and b/inst/extdata/testdata/GSE26682.GPL96_eset.rda differ
diff --git a/inst/extdata/testdata/GSE26906_eset.rda b/inst/extdata/testdata/GSE26906_eset.rda
new file mode 100644
index 0000000..58d555b
Binary files /dev/null and b/inst/extdata/testdata/GSE26906_eset.rda differ
diff --git a/inst/extdata/testdata/GSE27544_eset.rda b/inst/extdata/testdata/GSE27544_eset.rda
new file mode 100644
index 0000000..f20a7bb
Binary files /dev/null and b/inst/extdata/testdata/GSE27544_eset.rda differ
diff --git a/inst/extdata/testdata/GSE28702_eset.rda b/inst/extdata/testdata/GSE28702_eset.rda
new file mode 100644
index 0000000..e392cdd
Binary files /dev/null and b/inst/extdata/testdata/GSE28702_eset.rda differ
diff --git a/inst/extdata/testdata/GSE3294_eset.rda b/inst/extdata/testdata/GSE3294_eset.rda
new file mode 100644
index 0000000..d9cc980
Binary files /dev/null and b/inst/extdata/testdata/GSE3294_eset.rda differ
diff --git a/inst/extdata/testdata/GSE33113_eset.rda b/inst/extdata/testdata/GSE33113_eset.rda
new file mode 100644
index 0000000..2d8c006
Binary files /dev/null and b/inst/extdata/testdata/GSE33113_eset.rda differ
diff --git a/inst/extdata/testdata/GSE39582_eset.rda b/inst/extdata/testdata/GSE39582_eset.rda
new file mode 100644
index 0000000..f69e155
Binary files /dev/null and b/inst/extdata/testdata/GSE39582_eset.rda differ
diff --git a/inst/extdata/testdata/GSE3964_eset.rda b/inst/extdata/testdata/GSE3964_eset.rda
new file mode 100644
index 0000000..76634df
Binary files /dev/null and b/inst/extdata/testdata/GSE3964_eset.rda differ
diff --git a/inst/extdata/testdata/GSE4045_eset.rda b/inst/extdata/testdata/GSE4045_eset.rda
new file mode 100644
index 0000000..c1e0423
Binary files /dev/null and b/inst/extdata/testdata/GSE4045_eset.rda differ
diff --git a/inst/extdata/testdata/GSE4526_eset.rda b/inst/extdata/testdata/GSE4526_eset.rda
new file mode 100644
index 0000000..0ba3fee
Binary files /dev/null and b/inst/extdata/testdata/GSE4526_eset.rda differ
diff --git a/inst/extdata/testdata/GSE45270_eset.rda b/inst/extdata/testdata/GSE45270_eset.rda
new file mode 100644
index 0000000..c3cd524
Binary files /dev/null and b/inst/extdata/testdata/GSE45270_eset.rda differ
diff --git a/inst/extdata/testdata/TCGA.COAD_eset.rda b/inst/extdata/testdata/TCGA.COAD_eset.rda
new file mode 100644
index 0000000..bc1d297
Binary files /dev/null and b/inst/extdata/testdata/TCGA.COAD_eset.rda differ
diff --git a/inst/extdata/testdata/TCGA.READ_eset.rda b/inst/extdata/testdata/TCGA.READ_eset.rda
new file mode 100644
index 0000000..1a74d9e
Binary files /dev/null and b/inst/extdata/testdata/TCGA.READ_eset.rda differ
diff --git a/inst/extdata/testdata/TCGA.RNASeqV2.READ_eset.rda b/inst/extdata/testdata/TCGA.RNASeqV2.READ_eset.rda
new file mode 100644
index 0000000..7ae667d
Binary files /dev/null and b/inst/extdata/testdata/TCGA.RNASeqV2.READ_eset.rda differ
diff --git a/inst/extdata/testdata/TCGA.RNASeqV2_eset.rda b/inst/extdata/testdata/TCGA.RNASeqV2_eset.rda
new file mode 100644
index 0000000..a29610b
Binary files /dev/null and b/inst/extdata/testdata/TCGA.RNASeqV2_eset.rda differ
diff --git a/inst/extdata/zenodo-manifest.csv b/inst/extdata/zenodo-manifest.csv
new file mode 100644
index 0000000..f61fa17
--- /dev/null
+++ b/inst/extdata/zenodo-manifest.csv
@@ -0,0 +1,35 @@
+dataset,filename,url,md5,size_bytes
+GSE11237_eset,GSE11237_eset.rda,https://zenodo.org/records/23125734/files/GSE11237_eset.rda?download=1,307f4c572b663edaa8c65e620498d8e5,1462208
+GSE12225.GPL3676_eset,GSE12225.GPL3676_eset.rda,https://zenodo.org/records/23125734/files/GSE12225.GPL3676_eset.rda?download=1,ba5e2d45c597ae6e166fbfc7ce27ba44,1321808
+GSE12945_eset,GSE12945_eset.rda,https://zenodo.org/records/23125734/files/GSE12945_eset.rda?download=1,06747a29b28a2f3599c25d53cf1acbf5,5676968
+GSE13067_eset,GSE13067_eset.rda,https://zenodo.org/records/23125734/files/GSE13067_eset.rda?download=1,9ea4179c37ab2eea0f5779b9e5b9f8ef,10096264
+GSE13294_eset,GSE13294_eset.rda,https://zenodo.org/records/23125734/files/GSE13294_eset.rda?download=1,5919e1903d672ebb074ea98c5c773703,6862824
+GSE14095_eset,GSE14095_eset.rda,https://zenodo.org/records/23125734/files/GSE14095_eset.rda?download=1,902d4872308ee51e0764015fac2b062c,6909552
+GSE14333_eset,GSE14333_eset.rda,https://zenodo.org/records/23125734/files/GSE14333_eset.rda?download=1,ccc1735fb1d9f664afa77fc5d801d8b8,12431512
+GSE16125.GPL5175_eset,GSE16125.GPL5175_eset.rda,https://zenodo.org/records/23125734/files/GSE16125.GPL5175_eset.rda?download=1,aba783ba87e66bde68e5307a120c1a2e,1080260
+GSE17536_eset,GSE17536_eset.rda,https://zenodo.org/records/23125734/files/GSE17536_eset.rda?download=1,bbdaf3e0d0c3682e2daf9fe19d2a41ed,18625140
+GSE17537_eset,GSE17537_eset.rda,https://zenodo.org/records/23125734/files/GSE17537_eset.rda?download=1,0f47e4d4adf5815c0cb7f04e21fa9f25,7545656
+GSE17538.GPL570_eset,GSE17538.GPL570_eset.rda,https://zenodo.org/records/23125734/files/GSE17538.GPL570_eset.rda?download=1,659686dcd2a78d7726f8d21894384b65,23588252
+GSE18105_eset,GSE18105_eset.rda,https://zenodo.org/records/23125734/files/GSE18105_eset.rda?download=1,b7d2e879f1fef1ef8e0c0a184e09a52c,15109988
+GSE2109_eset,GSE2109_eset.rda,https://zenodo.org/records/23125734/files/GSE2109_eset.rda?download=1,9124df5c503a1e020b789a6c2cb3521f,18402064
+GSE21510_eset,GSE21510_eset.rda,https://zenodo.org/records/23125734/files/GSE21510_eset.rda?download=1,fa48020c10885777624d7007fb5f2896,20090392
+GSE21815_eset,GSE21815_eset.rda,https://zenodo.org/records/23125734/files/GSE21815_eset.rda?download=1,8739e1111a1604c4d733d58a270a241c,18108200
+GSE24549.GPL5175_eset,GSE24549.GPL5175_eset.rda,https://zenodo.org/records/23125734/files/GSE24549.GPL5175_eset.rda?download=1,b41298ddb66e3703352867ce8f2391e2,2379240
+GSE24550.GPL5175_eset,GSE24550.GPL5175_eset.rda,https://zenodo.org/records/23125734/files/GSE24550.GPL5175_eset.rda?download=1,3df5a16f0d90505439f92b92608aac58,2555172
+GSE2630_eset,GSE2630_eset.rda,https://zenodo.org/records/23125734/files/GSE2630_eset.rda?download=1,c650169bc58e13b6a1be326155c2a2a4,543940
+GSE26682.GPL570_eset,GSE26682.GPL570_eset.rda,https://zenodo.org/records/23125734/files/GSE26682.GPL570_eset.rda?download=1,4a552232901ae8036e2d390211ac66cd,3762880
+GSE26682.GPL96_eset,GSE26682.GPL96_eset.rda,https://zenodo.org/records/23125734/files/GSE26682.GPL96_eset.rda?download=1,440c10c04fa09fe56c650f5dcfad84fb,14050244
+GSE26906_eset,GSE26906_eset.rda,https://zenodo.org/records/23125734/files/GSE26906_eset.rda?download=1,3399ec7149ef6a76a7e6d77a21ba36bb,12271168
+GSE27544_eset,GSE27544_eset.rda,https://zenodo.org/records/23125734/files/GSE27544_eset.rda?download=1,ca61888b627394a753d6f93e6ea0eb08,1399976
+GSE28702_eset,GSE28702_eset.rda,https://zenodo.org/records/23125734/files/GSE28702_eset.rda?download=1,852f42b9d3ee28d3bc6076747df5aa38,11314752
+GSE3294_eset,GSE3294_eset.rda,https://zenodo.org/records/23125734/files/GSE3294_eset.rda?download=1,f8f62bce4fa9f8d8c27a8331defb118c,684632
+GSE33113_eset,GSE33113_eset.rda,https://zenodo.org/records/23125734/files/GSE33113_eset.rda?download=1,9814126b6fc740de2713e1fec4b15782,13066544
+GSE39582_eset,GSE39582_eset.rda,https://zenodo.org/records/23125734/files/GSE39582_eset.rda?download=1,7bdbbadfaa9d4ff88bdc791042287a9f,53940012
+GSE3964_eset,GSE3964_eset.rda,https://zenodo.org/records/23125734/files/GSE3964_eset.rda?download=1,0a73a4dda729f2dfccb26d658d6cbb8a,1308480
+GSE4045_eset,GSE4045_eset.rda,https://zenodo.org/records/23125734/files/GSE4045_eset.rda?download=1,55536e548b97689ad3fd7ab44fb33418,3432252
+GSE4526_eset,GSE4526_eset.rda,https://zenodo.org/records/23125734/files/GSE4526_eset.rda?download=1,194e39c56aa6e63eb926fd2d02c1b8e8,4499620
+GSE45270_eset,GSE45270_eset.rda,https://zenodo.org/records/23125734/files/GSE45270_eset.rda?download=1,0b1203cb8c724a0b5e8e33b63264ef94,1866416
+TCGA.COAD_eset,TCGA.COAD_eset.rda,https://zenodo.org/records/23125734/files/TCGA.COAD_eset.rda?download=1,4865921e88a3e140dc33535df3d9ff47,5730984
+TCGA.READ_eset,TCGA.READ_eset.rda,https://zenodo.org/records/23125734/files/TCGA.READ_eset.rda?download=1,d1a6688d116f0b5a4229d4d427efb8a5,2326880
+TCGA.RNASeqV2_eset,TCGA.RNASeqV2_eset.rda,https://zenodo.org/records/23125734/files/TCGA.RNASeqV2_eset.rda?download=1,982129545ba576976d54e63e2e9077a8,12831588
+TCGA.RNASeqV2.READ_eset,TCGA.RNASeqV2.READ_eset.rda,https://zenodo.org/records/23125734/files/TCGA.RNASeqV2.READ_eset.rda?download=1,b7e99d4b002ac703ca19cb508d91a5e8,525084
diff --git a/inst/scripts/data-integrity-report.Rmd b/inst/scripts/data-integrity-report.Rmd
new file mode 100644
index 0000000..30fc9a8
--- /dev/null
+++ b/inst/scripts/data-integrity-report.Rmd
@@ -0,0 +1,91 @@
+---
+title: "Data integrity report: Zenodo offloading"
+output: html_document
+params:
+  package: "curatedCRCData"
+  upload_dir: "../../../curatedCRCData-zenodo-upload"
+---
+
+<!-- Verifies the Zenodo data offloading, run manually from inst/scripts/
+     of a package checkout (not built with the package vignettes):
+
+     1. every xz re-serialized object uploaded to Zenodo is identical to
+        the object shipped in the last pre-refactor package version
+        (git tag pre-zenodo-refactor);
+     2. the md5 checksums in inst/extdata/zenodo-manifest.csv match both
+        the local upload files and the checksums Zenodo reports;
+     3. one real download through the getter works and hits the cache on
+        the second call.
+
+     Because the manifest md5s equal the md5s of byte-identical uploads,
+     passing 1 + 2 proves every Zenodo file; only one download needs to
+     be exercised end to end.
+
+     NOTE: intentionally duplicated in curatedOvarianData. -->
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+suppressPackageStartupMessages(library(Biobase))
+pkg <- params$package
+stopifnot(requireNamespace(pkg))
+```
+
+# 1. Uploaded objects vs pre-refactor package objects
+
+```{r compare-objects}
+pre <- tempfile("pre-refactor-")
+system2("git", c("worktree", "add", "--detach", pre, "pre-zenodo-refactor"),
+        stdout = FALSE)
+
+manifest <- read.csv(file.path("..", "extdata", "zenodo-manifest.csv"))
+loadOne <- function(path) {
+    env <- new.env(); nm <- load(path, envir = env); get(nm[1], envir = env)
+}
+cmp <- vapply(manifest$dataset, function(nm) {
+    old <- loadOne(file.path(pre, "data", paste0(nm, ".rda")))
+    new <- loadOne(file.path(params$upload_dir, paste0(nm, ".rda")))
+    isTRUE(all.equal(exprs(old), exprs(new))) &&
+        isTRUE(all.equal(pData(old), pData(new))) &&
+        isTRUE(all.equal(fData(old), fData(new))) &&
+        identical(annotation(old), annotation(new)) &&
+        isTRUE(all.equal(experimentData(old), experimentData(new)))
+}, logical(1))
+system2("git", c("worktree", "remove", "--force", pre))
+data.frame(dataset = manifest$dataset, identical = cmp)
+stopifnot(all(cmp))
+```
+
+# 2. Manifest md5s vs local uploads and Zenodo
+
+```{r compare-md5}
+local_md5 <- tools::md5sum(file.path(params$upload_dir, manifest$filename))
+stopifnot(identical(unname(local_md5), manifest$md5))
+
+record <- unique(sub(".*records/([0-9A-Za-z_]+)/.*", "\\1", manifest$url))
+stopifnot(length(record) == 1L)
+api <- jsonlite::fromJSON(paste0("https://zenodo.org/api/records/", record))
+zen <- data.frame(filename = api$files$key,
+                  md5 = sub("^md5:", "", api$files$checksum))
+merged <- merge(manifest[, c("filename", "md5")], zen, by = "filename",
+                suffixes = c(".manifest", ".zenodo"))
+stopifnot(nrow(merged) == nrow(manifest),
+          identical(merged$md5.manifest, merged$md5.zenodo))
+merged
+```
+
+# 3. Download smoke test
+
+```{r smoke-test}
+getter <- get(pkg, envir = asNamespace(pkg))
+smallest <- manifest$dataset[which.min(manifest$size_bytes)]
+unlink(tools::R_user_dir(pkg, "cache"), recursive = TRUE)
+eset <- getter(smallest)              # downloads
+stopifnot(is(eset, "ExpressionSet"))
+eset2 <- getter(smallest)             # must hit the cache silently
+stopifnot(identical(dim(eset), dim(eset2)))
+dim(eset)
+```
+
+```{r session-info}
+sessionInfo()
+```
diff --git a/inst/scripts/make-data.R b/inst/scripts/make-data.R
new file mode 100644
index 0000000..aa6d536
--- /dev/null
+++ b/inst/scripts/make-data.R
@@ -0,0 +1,68 @@
+## Prepare the per-dataset .rda files uploaded to Zenodo, along with the
+## download manifest, the data/ stub files, and data/datalist.
+##
+## The datasets themselves were produced by the curatedCRCData curation
+## pipeline (see the package vignette and inst/extdata/template_crc.csv);
+## this script re-serializes the .rda files that shipped inside the package
+## through version 2.45.x (git tag: pre-zenodo-refactor) with xz compression
+## for hosting on Zenodo.
+##
+## Run from the package root with the full data/*.rda files present:
+##   Rscript inst/scripts/make-data.R            # before upload (placeholder URLs)
+##   Rscript inst/scripts/make-data.R <RECORD>   # after publishing, to finalize URLs
+## Already-compressed files in the output directory are left untouched, so
+## re-running with the record ID only rewrites the manifest. Do NOT
+## regenerate the .rda files after uploading (checksums must match Zenodo).
+##
+## NOTE: this script is intentionally duplicated in curatedOvarianData.
+
+pkg <- unname(read.dcf("DESCRIPTION")[, "Package"])
+record <- commandArgs(trailingOnly = TRUE)
+record <- if (length(record)) record[1L] else "RECORD_ID"
+
+outdir <- file.path("..", paste0(pkg, "-zenodo-upload"))
+stubdir <- file.path(outdir, "stubs")
+dir.create(stubdir, recursive = TRUE, showWarnings = FALSE)
+
+## enumerate from data/ before the refactor, or from the already-compressed
+## upload directory when re-running to finalize URLs
+rdas <- sort(list.files("data", pattern = "\\.rda$"))
+if (length(rdas) == 0L)
+    rdas <- sort(list.files(outdir, pattern = "\\.rda$"))
+stopifnot(length(rdas) > 0L)
+
+rows <- lapply(rdas, function(f) {
+    nm <- sub("\\.rda$", "", f)
+    out <- file.path(outdir, f)
+    if (!file.exists(out)) {
+        env <- new.env(parent = emptyenv())
+        obj <- load(file.path("data", f), envir = env)
+        stopifnot(identical(obj, nm))
+        save(list = nm, envir = env, file = out, compress = "xz")
+        message("compressed ", f)
+    }
+    writeLines(sprintf(
+        'delayedAssign("%s",\n    %s:::.stubLoad("%s"),\n    assign.env = environment())',
+        nm, pkg, nm),
+        file.path(stubdir, paste0(nm, ".R")))
+    data.frame(dataset = nm, filename = f,
+        url = sprintf("https://zenodo.org/records/%s/files/%s?download=1",
+                      record, f),
+        md5 = unname(tools::md5sum(out)), size_bytes = file.size(out))
+})
+manifest <- do.call(rbind, rows)
+
+write.csv(manifest, file.path(outdir, "zenodo-manifest.csv"),
+          row.names = FALSE, quote = FALSE)
+writeLines(manifest$dataset, file.path(stubdir, "datalist"))
+writeLines(sprintf("%s  %12d  %s", manifest$md5, manifest$size_bytes,
+                   manifest$filename),
+           file.path(outdir, "upload-manifest.txt"))
+
+message(nrow(manifest), " datasets; total upload size ",
+        round(sum(manifest$size_bytes) / 2^20), " MB; written to ", outdir)
+if (identical(record, "RECORD_ID"))
+    message("Upload the .rda files to a new Zenodo record, publish it, ",
+            "verify the md5s shown by Zenodo against upload-manifest.txt, ",
+            "then re-run this script with the record ID and copy ",
+            "zenodo-manifest.csv to inst/extdata/.")
diff --git a/inst/scripts/make-test-data.R b/inst/scripts/make-test-data.R
new file mode 100644
index 0000000..f0ebe97
--- /dev/null
+++ b/inst/scripts/make-test-data.R
@@ -0,0 +1,39 @@
+## Build the small offline test fixtures in inst/extdata/testdata/: one per
+## dataset, subset to the first <=200 features and <=100 samples with full
+## phenoData retained, so that examples, tests, vignettes, and R CMD check
+## run without network access (see the test= argument of the getter and
+## .stubLoad in R/getData.R).
+##
+## Run from the package root with the full data/*.rda files present
+## (git tag: pre-zenodo-refactor):
+##   Rscript inst/scripts/make-test-data.R
+##
+## NOTE: this script is intentionally duplicated in curatedOvarianData.
+
+suppressPackageStartupMessages(library(Biobase))
+
+dir.create("inst/extdata/testdata", recursive = TRUE, showWarnings = FALSE)
+rdas <- sort(list.files("data", pattern = "\\.rda$"))
+stopifnot(length(rdas) > 0L)
+
+for (f in rdas) {
+    nm <- sub("\\.rda$", "", f)
+    env <- new.env(parent = emptyenv())
+    obj <- load(file.path("data", f), envir = env)
+    stopifnot(identical(obj, nm))
+    eset <- get(nm, envir = env)
+    ## keep the first ~200 features plus genes used in the vignettes
+    ## (survival forest plots, probe-expansion examples)
+    fn <- featureNames(eset)
+    keep <- unique(c(intersect(c("CXCL12", "CXCR4"), fn),
+                     head(grep("///", fn, value = TRUE), 5L),
+                     head(fn, 200L)))
+    fx <- eset[keep, seq_len(min(100L, ncol(eset)))]
+    assign(nm, fx)
+    save(list = nm, file = file.path("inst/extdata/testdata", f),
+         compress = "xz")
+    message("fixture ", nm, ": ", nrow(fx), " x ", ncol(fx))
+}
+message("total fixture size: ",
+        round(sum(file.size(list.files("inst/extdata/testdata",
+                                       full.names = TRUE))) / 2^10), " KB")
diff --git a/inst/unitTests/test_checkCurated.R b/inst/unitTests/test_checkCurated.R
deleted file mode 100644
index 4567d49..0000000
--- a/inst/unitTests/test_checkCurated.R
+++ /dev/null
@@ -1,105 +0,0 @@
-test_checkCurated <- function(){
-    library(affy)
-    ##the template to use
-    ##template.file <- "../extdata/template_ov.csv"
-    template.file <- system.file("extdata/template_crc.csv", package = "curatedCRCData")
-    template <- read.csv(template.file, as.is=TRUE)
-
-    ##get rid of the first row of template - this is sample_name
-    template <- template[-1, ]
-
-    ##the list of datasets to check
-    dataset.names <- data(package="curatedCRCData")$results[, "Item"]
-
-    ##Create a checklist for three checks in all files
-    checklist <- matrix(NA,ncol=2,nrow=length(dataset.names))
-    colnames(checklist) <- c("column.names","variable.regex.checks")
-    rownames(checklist) <- dataset.names
-
-    ##Make a list of curated metadata:
-    curated <- lapply(dataset.names, function(x){
-        data(list=x, package="curatedCRCData")
-        pData(get(x))
-    })
-    names(curated) <- dataset.names
-
-
-    ##-------------------------------------------------
-    ##check that the column names match the template
-    ##-------------------------------------------------
-    for (i in 1:length(curated)){
-        print(paste("Checking column names in",dataset.names[i]))
-        ##check column names
-        if(identical(all.equal(colnames(curated[[i]]),template$col.name),TRUE)){
-            print("column names OK")
-            checklist[i,"column.names"] <- TRUE
-        }else{
-            all.equal(colnames(curated[[i]]),template$col.name)
-            print("Column names should be: ")
-            print(template$col.name)
-            print("Column names are: ")
-            print(colnames(curated[[i]]))
-            checklist[i,"column.names"] <- FALSE
-        }
-    }
-
-    ##-------------------------------------------------
-    ##construct the regexes from template$allowedvalues
-    ##-------------------------------------------------
-    regexes <- template$allowedvalues
-    regexes <- paste("^",regexes,"$",sep="")
-    regexes <- gsub("|","$|^",regexes,fixed=TRUE)
-    ##regexes[template$requiredness=="optional"] <- paste(regexes[template$requiredness=="optional"],"|^NA$",sep="")
-    regexes[grep("^*$",regexes,fixed=TRUE)] <- "."
-    names(regexes) <- template$col.name
-    regexes[grep("decimal",regexes)] <- "^[0-9]+\\.?[0-9]*$"
-
-    ##-------------------------------------------------
-    ##Check the data entries in each column for regex
-    ## matching, uniqueness, and missingness
-    ##-------------------------------------------------
-    for (i in which(checklist[,"column.names"])){
-        print(paste("Checking regexes in",dataset.names[i]))
-        ##check column names
-        column.OK <- rep(NA,ncol(curated[[i]]))
-        names(column.OK) <- colnames(curated[[i]])
-        for(j in 1:ncol(curated[[i]])){
-            doesmatch <- grep(regexes[j],curated[[i]][,j])
-            if(template[j,"requiredness"]=="optional"){
-                doesmatch <- c(doesmatch,which(is.na(curated[[i]][,j])))
-            }
-            doesnotmatch <- 1:nrow(curated[[i]])
-            doesnotmatch <- doesnotmatch[!doesnotmatch %in% doesmatch]
-            ## if field must be unique, add non-unique values to doesnotmatch
-            if(template[j,"uniqueness"]=="unique"){
-                counts.table <- table(curated[[i]][,j])
-                counts <- counts.table[match(curated[[i]][,j],names(counts.table))]  #this counts the occurences
-                counts[is.na(counts)] <- 1  ##Consider NAs to be unique
-                nonunique <- which(counts>1)
-                doesnotmatch <- c(doesnotmatch,nonunique)
-                doesnotmatch <- unique(doesnotmatch)  #don't duplicate fields which fail both tests
-            }
-            if(length(doesnotmatch)==0){
-                column.OK[j] <- TRUE
-            }else{
-                column.OK[j] <- FALSE
-                curated[[i]][doesnotmatch,j] <- paste("!!!",curated[[i]][doesnotmatch,j],"!!!",sep="")
-            }
-        }
-        if(all(column.OK)){
-            print("all regex checks OK")
-            checklist[i,"variable.regex.checks"] <- TRUE
-        }else{
-            print(paste("The following columns failed the regex check for ",dataset.names[i],":",sep=""))
-            print(names(column.OK)[!column.OK])
-            print(curated[[i]][,!column.OK])
-            checklist[i,"variable.regex.checks"] <- FALSE
-        }
-    }
-
-    print(checklist)
-
-    checkTrue( all(checklist[, "column.names"]) )
-    checkTrue( all(checklist[, "variable.regex.checks"]) )
-
-}
diff --git a/inst/unitTests/test_checkCurated.Rout b/inst/unitTests/test_checkCurated.Rout
deleted file mode 100644
index 5b3037e..0000000
--- a/inst/unitTests/test_checkCurated.Rout
+++ /dev/null
@@ -1,128 +0,0 @@
-
-R version 3.0.1 (2013-05-16) -- "Good Sport"
-Copyright (C) 2013 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
-  Natural language support but running in an English locale
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
-> test_checkCurated <- function(){
-+     library(affy)
-+     ##the template to use
-+     ##template.file <- "../extdata/template_ov.csv"
-+     template.file <- system.file("extdata/template_crc.csv", package = "curatedCRCData")
-+     template <- read.csv(template.file, as.is=TRUE)
-+ 
-+     ##get rid of the first row of template - this is sample_name
-+     template <- template[-1, ]
-+ 
-+     ##the list of datasets to check
-+     dataset.names <- data(package="curatedCRCData")$results[, "Item"]
-+ 
-+     ##Create a checklist for three checks in all files
-+     checklist <- matrix(NA,ncol=2,nrow=length(dataset.names))
-+     colnames(checklist) <- c("column.names","variable.regex.checks")
-+     rownames(checklist) <- dataset.names
-+ 
-+     ##Make a list of curated metadata:
-+     curated <- lapply(dataset.names, function(x){
-+         data(list=x, package="curatedCRCData")
-+         pData(get(x))
-+     })
-+     names(curated) <- dataset.names
-+ 
-+ 
-+     ##-------------------------------------------------
-+     ##check that the column names match the template
-+     ##-------------------------------------------------
-+     for (i in 1:length(curated)){
-+         print(paste("Checking column names in",dataset.names[i]))
-+         ##check column names
-+         if(identical(all.equal(colnames(curated[[i]]),template$col.name),TRUE)){
-+             print("column names OK")
-+             checklist[i,"column.names"] <- TRUE
-+         }else{
-+             all.equal(colnames(curated[[i]]),template$col.name)
-+             print("Column names should be: ")
-+             print(template$col.name)
-+             print("Column names are: ")
-+             print(colnames(curated[[i]]))
-+             checklist[i,"column.names"] <- FALSE
-+         }
-+     }
-+ 
-+     ##-------------------------------------------------
-+     ##construct the regexes from template$allowedvalues
-+     ##-------------------------------------------------
-+     regexes <- template$allowedvalues
-+     regexes <- paste("^",regexes,"$",sep="")
-+     regexes <- gsub("|","$|^",regexes,fixed=TRUE)
-+     ##regexes[template$requiredness=="optional"] <- paste(regexes[template$requiredness=="optional"],"|^NA$",sep="")
-+     regexes[grep("^*$",regexes,fixed=TRUE)] <- "."
-+     names(regexes) <- template$col.name
-+     regexes[grep("decimal",regexes)] <- "^[0-9]+\\.?[0-9]*$"
-+ 
-+     ##-------------------------------------------------
-+     ##Check the data entries in each column for regex
-+     ## matching, uniqueness, and missingness
-+     ##-------------------------------------------------
-+     for (i in which(checklist[,"column.names"])){
-+         print(paste("Checking regexes in",dataset.names[i]))
-+         ##check column names
-+         column.OK <- rep(NA,ncol(curated[[i]]))
-+         names(column.OK) <- colnames(curated[[i]])
-+         for(j in 1:ncol(curated[[i]])){
-+             doesmatch <- grep(regexes[j],curated[[i]][,j])
-+             if(template[j,"requiredness"]=="optional"){
-+                 doesmatch <- c(doesmatch,which(is.na(curated[[i]][,j])))
-+             }
-+             doesnotmatch <- 1:nrow(curated[[i]])
-+             doesnotmatch <- doesnotmatch[!doesnotmatch %in% doesmatch]
-+             ## if field must be unique, add non-unique values to doesnotmatch
-+             if(template[j,"uniqueness"]=="unique"){
-+                 counts.table <- table(curated[[i]][,j])
-+                 counts <- counts.table[match(curated[[i]][,j],names(counts.table))]  #this counts the occurences
-+                 counts[is.na(counts)] <- 1  ##Consider NAs to be unique
-+                 nonunique <- which(counts>1)
-+                 doesnotmatch <- c(doesnotmatch,nonunique)
-+                 doesnotmatch <- unique(doesnotmatch)  #don't duplicate fields which fail both tests
-+             }
-+             if(length(doesnotmatch)==0){
-+                 column.OK[j] <- TRUE
-+             }else{
-+                 column.OK[j] <- FALSE
-+                 curated[[i]][doesnotmatch,j] <- paste("!!!",curated[[i]][doesnotmatch,j],"!!!",sep="")
-+             }
-+         }
-+         if(all(column.OK)){
-+             print("all regex checks OK")
-+             checklist[i,"variable.regex.checks"] <- TRUE
-+         }else{
-+             print(paste("The following columns failed the regex check for ",dataset.names[i],":",sep=""))
-+             print(names(column.OK)[!column.OK])
-+             print(curated[[i]][,!column.OK])
-+             checklist[i,"variable.regex.checks"] <- FALSE
-+         }
-+     }
-+ 
-+     print(checklist)
-+ 
-+     checkTrue( all(checklist[, "column.names"]) )
-+     checkTrue( all(checklist[, "variable.regex.checks"]) )
-+ 
-+ }
-> 
-> proc.time()
-   user  system elapsed 
-  0.224   0.028   0.244 
diff --git a/inst/unitTests/test_counts.R b/inst/unitTests/test_counts.R
deleted file mode 100755
index 36e9457..0000000
--- a/inst/unitTests/test_counts.R
+++ /dev/null
@@ -1,25 +0,0 @@
-test_counts <- function() {
-    require(curatedCRCData)
-    require(affy)
-    strEsets <- data(package="curatedCRCData")[[3]][,3]
-    esets <- lapply(strEsets, function(x){
-        data(list=x)
-        get(x)
-    })
-    df <- data.frame(PMID=sapply(esets, pubMedIds), 
-                     ncol=sapply(esets,ncol),
-                     nrow=sapply(esets,nrow),
-                     nwithbatch=sapply(esets, function(x) sum(!is.na(x$batch))),
-                     deceased=sapply(esets,function(X)
-                               sum(X$vital_status=="deceased",na.rm=TRUE)),
-                     stringsAsFactors = FALSE)
-    df = df[order(df$PMID, df$ncol, df$nrow),]
-    ## reference file was generated with the following commands on 1.2.0:
-    ##  write.csv(df, file="../extdata/curatedOvarianData_counts.csv", quote=TRUE, row.names=FALSE)
-    ## dfref <- read.csv("../extdata/curatedOvarianData_counts.csv", as.is=TRUE)
-    dfref <- read.csv(system.file("extdata/curatedCRCData_counts.csv", package = "curatedCRCData"), as.is=TRUE)
-    sapply(1:ncol(df), function(i){
-        df[df[, i] != dfref[ ,i], i] <- paste("!!!", df[df[, i] != dfref[ ,i], i], "!!!", sep="")
-        print(data.frame(i, df[, i], dfref[, i]))
-        checkEquals(as.character(df[,i]), as.character(dfref[,i]))})
-}
diff --git a/man/curatedCRCData-package.Rd b/man/curatedCRCData-package.Rd
index d020bc6..5d20384 100644
--- a/man/curatedCRCData-package.Rd
+++ b/man/curatedCRCData-package.Rd
@@ -1,32 +1,28 @@
 \name{curatedCRCData-package}
-\alias{curatedCRCData}
+\alias{curatedCRCData-package}
 \docType{package}
 \title{Clinically Annotated Data for the CRC Cancer Transcriptome}
 \description{The curatedCRCData package provides manually curated
-  clinical data, uniformly processed expression data, and convenience
-  functions for gene expression analysis in patients with colorectal cancer.
-  
+  clinical data and uniformly processed expression data for gene
+  expression analysis in patients with colorectal cancer.
+
   Note: For staging, the "summarystage" was curated as using information on the pathologic T, N, and M stages, such that "early" = T stage of Tis through T3 and N0 and M0 and "late" = T stage of 4 and/or any N>0 or M>0}
 \details{
-\tabular{ll}{
-Package: \tab curatedCRCData\cr
-Type: \tab Package\cr
-Version: \tab \Sexpr{packageDescription("curatedCRCData")$Version}\cr
-Date: \tab \Sexpr{packageDescription("curatedCRCData")$Date}\cr
-License: \tab Artistic-2.0\cr
-Depends: \tab R (>= 2.10.0), affy\cr
-}
+  Datasets are hosted on Zenodo and downloaded on first use with
+  \code{\link{curatedCRCData}()}, which caches them locally with
+  \pkg{BiocFileCache}. Legacy \code{data()} access still works but is
+  deprecated and downloads through the same mechanism. See the package
+  vignette for rule-based creation of a list of filtered datasets.
 }
 \author{
-Princy Parsana, Markus Riester, Levi Waldron
+Princy Parsana, Markus Riester, Curtis Huttenhower, Levi Waldron
 
-Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health
-
-Maintainer: Princy Parsana <princyparsana@jhu.edu>
+Maintainer: Levi Waldron <lwaldron.research@gmail.com>
 }
-
 \examples{
-##List all datasets:
-data(package="curatedCRCData")
-##
+## List all datasets:
+curatedCRCData()
+## Load one dataset (test=TRUE uses a small offline subset):
+eset <- curatedCRCData("GSE3294_eset", test = TRUE)
 }
+\keyword{package}
diff --git a/man/curatedCRCData.Rd b/man/curatedCRCData.Rd
new file mode 100644
index 0000000..2f62ec1
--- /dev/null
+++ b/man/curatedCRCData.Rd
@@ -0,0 +1,40 @@
+\name{curatedCRCData}
+\alias{curatedCRCData}
+\title{Download curated colorectal cancer ExpressionSets}
+\description{
+  Datasets are hosted on Zenodo and downloaded individually on first use,
+  then cached locally with \pkg{BiocFileCache}; later calls load from the
+  cache without network access. Loading datasets with \code{data()} still
+  works but is deprecated in favor of this function.
+}
+\usage{
+curatedCRCData(datasets, test = FALSE)
+}
+\arguments{
+  \item{datasets}{Character vector of dataset names (e.g.
+    \code{"GSE39582_eset"}). If missing, the names of all available
+    datasets are returned and nothing is downloaded.}
+  \item{test}{If \code{TRUE}, load small offline test subsets bundled
+    with the package instead of downloading the full datasets. Intended
+    for examples, tests, and vignettes; the subsets are not suitable
+    for analysis.}
+}
+\value{
+  A single \code{\linkS4class{ExpressionSet}} if one dataset name is
+  given; a named list of \code{ExpressionSet}s if several; a character
+  vector of available dataset names if \code{datasets} is missing.
+}
+\details{
+  Downloaded files are stored in a package-specific cache directory
+  (\code{tools::R_user_dir("curatedCRCData", "cache")}). To remove
+  cached files, delete that directory or manage it with
+  \pkg{BiocFileCache}.
+}
+\examples{
+curatedCRCData()  # list available datasets
+eset <- curatedCRCData("GSE3294_eset", test = TRUE)
+dim(eset)
+esets <- curatedCRCData(c("GSE2630_eset", "GSE3294_eset"), test = TRUE)
+names(esets)
+}
+\keyword{utilities}
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..e62ed5e
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,4 @@
+library(testthat)
+library(curatedCRCData)
+
+test_check("curatedCRCData")
diff --git a/tests/testthat/test-getData.R b/tests/testthat/test-getData.R
new file mode 100644
index 0000000..0428fb8
--- /dev/null
+++ b/tests/testthat/test-getData.R
@@ -0,0 +1,77 @@
+# The 34 datasets this package has provided since its initial release; this
+# list guards the Zenodo manifest against accidental row loss.
+expected_datasets <- c(
+    "GSE11237_eset", "GSE12225.GPL3676_eset", "GSE12945_eset",
+    "GSE13067_eset", "GSE13294_eset", "GSE14095_eset", "GSE14333_eset",
+    "GSE16125.GPL5175_eset", "GSE17536_eset", "GSE17537_eset",
+    "GSE17538.GPL570_eset", "GSE18105_eset", "GSE2109_eset",
+    "GSE21510_eset", "GSE21815_eset", "GSE24549.GPL5175_eset",
+    "GSE24550.GPL5175_eset", "GSE2630_eset", "GSE26682.GPL570_eset",
+    "GSE26682.GPL96_eset", "GSE26906_eset", "GSE27544_eset",
+    "GSE28702_eset", "GSE3294_eset", "GSE33113_eset", "GSE39582_eset",
+    "GSE3964_eset", "GSE4045_eset", "GSE4526_eset", "GSE45270_eset",
+    "TCGA.COAD_eset", "TCGA.READ_eset", "TCGA.RNASeqV2.READ_eset",
+    "TCGA.RNASeqV2_eset"
+)
+
+manifest <- read.csv(system.file("extdata", "zenodo-manifest.csv",
+                                 package = "curatedCRCData"))
+
+test_that("manifest is complete and well-formed", {
+    expect_setequal(manifest$dataset, expected_datasets)
+    expect_false(anyDuplicated(manifest$dataset) > 0)
+    expect_identical(manifest$filename, paste0(manifest$dataset, ".rda"))
+    expect_true(all(grepl("^[0-9a-f]{32}$", manifest$md5)))
+    expect_true(all(grepl(
+        "^https://zenodo\\.org/records/[0-9]+/files/.+\\?download=1$",
+        manifest$url)))
+    expect_true(all(manifest$size_bytes > 0))
+})
+
+test_that("manifest, fixtures, and data/ stubs are in lock-step", {
+    fixtures <- sub("\\.rda$", "", list.files(
+        system.file("extdata", "testdata", package = "curatedCRCData"),
+        pattern = "\\.rda$"))
+    expect_setequal(fixtures, expected_datasets)
+    stubs <- data(package = "curatedCRCData")$results[, "Item"]
+    expect_setequal(stubs, expected_datasets)
+})
+
+test_that("no-argument call lists the datasets", {
+    expect_setequal(curatedCRCData(), expected_datasets)
+})
+
+test_that("getter returns ExpressionSets from offline fixtures", {
+    eset <- curatedCRCData("GSE3294_eset", test = TRUE)
+    expect_s4_class(eset, "ExpressionSet")
+    expect_gt(ncol(eset), 0)
+    esets <- curatedCRCData(c("GSE2630_eset", "GSE3294_eset"), test = TRUE)
+    expect_type(esets, "list")
+    expect_named(esets, c("GSE2630_eset", "GSE3294_eset"))
+    expect_s4_class(esets[[1]], "ExpressionSet")
+})
+
+test_that("unknown dataset names give an informative error", {
+    expect_error(curatedCRCData("NOT_A_DATASET"), "Unknown dataset")
+    expect_error(curatedCRCData("NOT_A_DATASET", test = TRUE),
+                 "Unknown dataset")
+})
+
+test_that("data() stubs create a binding", {
+    e <- new.env()
+    data("GSE3294_eset", package = "curatedCRCData", envir = e)
+    expect_true(exists("GSE3294_eset", envir = e))
+})
+
+test_that("full download works (opt-in; set RUN_FULL_DOWNLOAD_TESTS=1)", {
+    skip_on_bioc()
+    skip_if(!nzchar(Sys.getenv("RUN_FULL_DOWNLOAD_TESTS")))
+    skip_if_offline("zenodo.org")
+    # smallest dataset in the collection
+    eset <- curatedCRCData("TCGA.RNASeqV2.READ_eset")
+    expect_s4_class(eset, "ExpressionSet")
+    # second call must hit the cache (no download message)
+    expect_silent(suppressMessages(
+        eset2 <- curatedCRCData("TCGA.RNASeqV2.READ_eset")))
+    expect_identical(dim(eset), dim(eset2))
+})
diff --git a/vignettes/curatedCRCData_vignette.Rmd b/vignettes/curatedCRCData_vignette.Rmd
index 8610ffd..5b48051 100644
--- a/vignettes/curatedCRCData_vignette.Rmd
+++ b/vignettes/curatedCRCData_vignette.Rmd
@@ -32,26 +32,47 @@ and clinical data formats.
 In this vignette, we give a short tour of the package and will show how to use
 it efficiently.
 
+# Data access and caching
+
+As of version 2.46, the datasets are no longer stored inside the package:
+they are hosted on [Zenodo](https://zenodo.org/) and downloaded
+individually the first time they are requested, then cached locally with
+`r BiocStyle::Biocpkg("BiocFileCache")` so later uses need no network
+access. The cache lives in a package-specific directory,
+`tools::R_user_dir("curatedCRCData", "cache")`; to reclaim disk space,
+delete that directory or manage it with *BiocFileCache*.
+
+The legacy `data(TCGA.COAD_eset)` syntax still works (it downloads
+through the same cache) but is deprecated and will be removed in a
+future release; please use the `curatedCRCData()` function shown below.
+
+Throughout this vignette we set `test = TRUE` (and `test.mode <- TRUE`),
+which loads small offline subsets of each dataset that are bundled with
+the package, so that the vignette builds without downloading data. For
+real analyses, omit these settings to work with the full datasets.
+
 # Load data sets
 Loading a single dataset is very easy. First we load the package:
 ```{r example1, message=FALSE, warning=FALSE}
 library(curatedCRCData)
 ```
 
-To get a listing of all the datasets, use the `data` function:
+To get a listing of all the datasets, call `curatedCRCData()` with no
+arguments:
 ```{r example1tcgastep2}
-data(package="curatedCRCData")
+curatedCRCData()
 ```
 
-Now to load a single dataset, we use the `data` function again:
+Now to load a single dataset (drop `test = TRUE` to download the full
+dataset):
 ```{r example1_load_tcga}
-data(TCGA.COAD_eset)
+TCGA.COAD_eset <- curatedCRCData("TCGA.COAD_eset", test = TRUE)
 TCGA.COAD_eset
 ```
 
 The datasets are provided as Bioconductor `ExpressionSet` objects and
 we refer to the Bioconductor documentation for users unfamiliar with this data
-structure. 
+structure.
 
 # Load datasets based on rules
 For a meta-analysis, we typically want to filter datasets and patients to
@@ -63,8 +84,9 @@ dataset. It is also possible to filter samples by annotation, for example to rem
 early stage and normal samples. 
 
 ```{r example2loadstep1}
-source(system.file("extdata", 
+source(system.file("extdata",
 "patientselection_all.config",package="curatedCRCData"))
+test.mode <- TRUE  # use the bundled offline subsets in this vignette
 ls()
 ```
 
@@ -193,7 +215,7 @@ a simple way to do it. For one dataset:
 ```{r simplygetdata, eval=FALSE}
 library(curatedCRCData)
 library(Biobase)
-data(TCGA.COAD_eset)
+TCGA.COAD_eset <- curatedCRCData("TCGA.COAD_eset")
 write.csv(exprs(TCGA.COAD_eset), file="TCGA.COAD_eset_exprs.csv")
 write.csv(pData(TCGA.COAD_eset), file="TCGA.COAD_eset_clindata.csv")
 ```
@@ -201,12 +223,12 @@ write.csv(pData(TCGA.COAD_eset), file="TCGA.COAD_eset_clindata.csv")
 Or for several datasets:
 
 ```{r simplyseveraldatasets, eval=FALSE}
-data.to.fetch <- c("TCGA.COAD_eset", "GSE37317_eset")
-for (onedata in data.to.fetch){
-    print(paste("Fetching", onedata))
-    data(list=onedata)
-    write.csv(exprs(get(onedata)), file=paste(onedata, "_exprs.csv", sep=""))
-    write.csv(pData(get(onedata)), file=paste(onedata, "_clindata.csv", sep=""))
+data.to.fetch <- curatedCRCData(c("TCGA.COAD_eset", "GSE39582_eset"))
+for (onedata in names(data.to.fetch)){
+    write.csv(exprs(data.to.fetch[[onedata]]),
+              file=paste(onedata, "_exprs.csv", sep=""))
+    write.csv(pData(data.to.fetch[[onedata]]),
+              file=paste(onedata, "_clindata.csv", sep=""))
 }
 ```