update pseudobulk download id

README.md

@@ -93,7 +93,7 @@ saved to `get_default_cache_dir()` unless a custom path is provided via
 the cache_directory argument. The `metadata` variable can then be
 re-used for all subsequent queries.
 
-The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21388944/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21388944](https://zenodo.org/records/21388944).
+The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21633607/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21633607](https://zenodo.org/records/21633607).
 
 The following sections demonstrate the metadata, quality control,
 generation of raw and normalised counts, and pseudobulk construction for
@@ -231,7 +231,7 @@ Reading counts ■■■■■■■■■■■■■■■■■■■■■
 
 single_cell_counts
 #> # A SingleCellExperiment-tibble abstraction: 2,806 × 60
-#> # Features=33145 | Cells=2806 | Assays=counts
+#> # [90mFeatures=33145 | Cells=2806 | Assays=counts[0m
 #>    .cell observation_joinid dataset_id     sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA
 #>    <chr> <chr>              <chr>          <chr>     <chr>   <chr>         <chr>            <chr>               <int> <chr>                          <int>      <dbl>
 #>  1 80_1  zz-!e5_XAo         842c6f5d-4a94… 1de3f3ba… 1de3f3… ""            <NA>             7fabaf1c-52fd-4…    14600 breast                          1749      10.8 
@@ -290,7 +290,7 @@ Reading cpm ■■■■■■■■■■■■■■■■■■■■■■
 
 single_cell_cpm
 #> # A SingleCellExperiment-tibble abstraction: 2,806 × 60
-#> # Features=33145 | Cells=2806 | Assays=cpm
+#> # [90mFeatures=33145 | Cells=2806 | Assays=cpm[0m
 #>    .cell observation_joinid dataset_id     sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA
 #>    <chr> <chr>              <chr>          <chr>     <chr>   <chr>         <chr>            <chr>               <int> <chr>                          <int>      <dbl>
 #>  1 80_1  zz-!e5_XAo         842c6f5d-4a94… 1de3f3ba… 1de3f3… ""            <NA>             7fabaf1c-52fd-4…    14600 breast                          1749      10.8 
@@ -363,7 +363,7 @@ Reading sct ■■■■■■■■■■■■■■■■■■■■■■
 
 single_cell_sct
 #> # A SingleCellExperiment-tibble abstraction: 1,193 × 60
-#> # Features=33145 | Cells=1193 | Assays=sct
+#> # [90mFeatures=33145 | Cells=1193 | Assays=sct[0m
 #>    .cell observation_joinid dataset_id     sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA
 #>    <chr> <chr>              <chr>          <chr>     <chr>   <chr>         <chr>            <chr>               <int> <chr>                          <int>      <dbl>
 #>  1 80_1  zz-!e5_XAo         842c6f5d-4a94… 1de3f3ba… 1de3f3… ""            <NA>             7fabaf1c-52fd-4…    14600 breast                          1749      10.8 
@@ -418,7 +418,7 @@ Reading counts ■■■■■■■■■■■■■■■■■■■■■
 
 pseudobulk_counts
 #> # A SingleCellExperiment-tibble abstraction: 139 × 43
-#> # Features=15888 | Cells=139 | Assays=counts
+#> # [90mFeatures=15888 | Cells=139 | Assays=counts[0m
 #>    .cell           dataset_id sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups cell_type_unified_en…¹ sample_chunk cell_chunk
 #>    <chr>           <chr>      <chr>     <chr>   <chr>         <chr>            <chr>               <int> <chr>         <chr>                         <int>      <int>
 #>  1 2e8c9911c9bfbf… 0ba16f4b-… 2e8c9911… 2e8c99… ""            <NA>             HDBR15279,HDBR1…       NA respiratory … cd14 mono                         1          1
@@ -517,7 +517,7 @@ Reading cpm ■■■■■■■■■■■■■■■■■■■■■■
 
 single_cell_cpm
 #> # A SingleCellExperiment-tibble abstraction: 2,806 × 60
-#> # Features=1 | Cells=2806 | Assays=cpm
+#> # [90mFeatures=1 | Cells=2806 | Assays=cpm[0m
 #>    .cell observation_joinid dataset_id     sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA
 #>    <chr> <chr>              <chr>          <chr>     <chr>   <chr>         <chr>            <chr>               <int> <chr>                          <int>      <dbl>
 #>  1 80_1  zz-!e5_XAo         842c6f5d-4a94… 1de3f3ba… 1de3f3… ""            <NA>             7fabaf1c-52fd-4…    14600 breast                          1749      10.8 
@@ -813,7 +813,7 @@ get_metadata(
 #> ℹ Reading files.
 #> ℹ Compiling Experiment.
 #> # A SingleCellExperiment-tibble abstraction: 500 × 7
-#> # Features=13132 | Cells=500 | Assays=counts
+#> # [90mFeatures=13132 | Cells=500 | Assays=counts[0m
 #>    .cell            sample_id dataset_id cell_type_unified_ensemble atlas_id             file_id_cellNexus_single_cell         original_cell_
 #>    <chr>            <chr>     <chr>      <chr>                      <chr>                <chr>                                 <chr>         
 #>  1 AAACATACAACCAC_1 pbmc3k    pbmc3k     Memory CD4 T               cellxgene/03-10-2025 67e196a3c4e145151fc9e06c200e2f7f.h5ad AAACATACAACCAC

index.md

@@ -61,7 +61,7 @@ The QC flags used throughout `cellNexus` are computed on sample-level using [HPC
 
 ## Metadata Explore
 
-Through harmonisation and curation, `cellNexus` adds columns that are not present in the original CELLxGENE metadata alone.
+Through harmonisation and curation, `cellNexus` adds columns that are not present in the original CELLxGENE metadata alone. The latest metadata is downloaded automatically when you call `get_metadata()` — no need to supply a download link manually. See the client usage examples for details on the columns available.
 
 | Column | Description |
 |--------|-------------|

vignettes/cellNexus.Rmd

@@ -84,7 +84,7 @@ suppressPackageStartupMessages({
 ### Load the metadata
 By default, `get_metadata()` loads harmonised annotations. Metadata is saved to `get_default_cache_dir()` unless a custom path is provided via the cache_directory argument. The `metadata` variable can then be re-used for all subsequent queries. 
 
-The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21388944/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21388944](https://zenodo.org/records/21388944).
+The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21633607/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21633607](https://zenodo.org/records/21633607).
 
 The following sections demonstrate the metadata, quality control, generation of raw and normalised counts, and pseudobulk construction for the specified query.
 
@@ -220,7 +220,7 @@ Reading counts â– â– â– â– â– â– â– â– â– â
 
 single_cell_counts
 #> # A SingleCellExperiment-tibble abstraction: 2,806 × 60
-#> # Features=33145 | Cells=2806 | Assays=counts
+#> # [90mFeatures=33145 | Cells=2806 | Assays=counts[0m
 #>    .cell observation_joinid dataset_id     sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA
 #>    <chr> <chr>              <chr>          <chr>     <chr>   <chr>         <chr>            <chr>               <int> <chr>                          <int>      <dbl>
 #>  1 80_1  zz-!e5_XAo         842c6f5d-4a94… 1de3f3ba… 1de3f3… ""            <NA>             7fabaf1c-52fd-4…    14600 breast                          1749      10.8 
@@ -280,7 +280,7 @@ Reading cpm â– â– â– â– â– â– â– â– â– â–
 
 single_cell_cpm
 #> # A SingleCellExperiment-tibble abstraction: 2,806 × 60
-#> # Features=33145 | Cells=2806 | Assays=cpm
+#> # [90mFeatures=33145 | Cells=2806 | Assays=cpm[0m
 #>    .cell observation_joinid dataset_id     sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA
 #>    <chr> <chr>              <chr>          <chr>     <chr>   <chr>         <chr>            <chr>               <int> <chr>                          <int>      <dbl>
 #>  1 80_1  zz-!e5_XAo         842c6f5d-4a94… 1de3f3ba… 1de3f3… ""            <NA>             7fabaf1c-52fd-4…    14600 breast                          1749      10.8 
@@ -353,7 +353,7 @@ Reading sct â– â– â– â– â– â– â– â– â– â–
 
 single_cell_sct
 #> # A SingleCellExperiment-tibble abstraction: 1,193 × 60
-#> # Features=33145 | Cells=1193 | Assays=sct
+#> # [90mFeatures=33145 | Cells=1193 | Assays=sct[0m
 #>    .cell observation_joinid dataset_id     sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA
 #>    <chr> <chr>              <chr>          <chr>     <chr>   <chr>         <chr>            <chr>               <int> <chr>                          <int>      <dbl>
 #>  1 80_1  zz-!e5_XAo         842c6f5d-4a94… 1de3f3ba… 1de3f3… ""            <NA>             7fabaf1c-52fd-4…    14600 breast                          1749      10.8 
@@ -408,7 +408,7 @@ Reading counts â– â– â– â– â– â– â– â– â– â
 
 pseudobulk_counts
 #> # A SingleCellExperiment-tibble abstraction: 139 × 43
-#> # Features=15888 | Cells=139 | Assays=counts
+#> # [90mFeatures=15888 | Cells=139 | Assays=counts[0m
 #>    .cell           dataset_id sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups cell_type_unified_en…¹ sample_chunk cell_chunk
 #>    <chr>           <chr>      <chr>     <chr>   <chr>         <chr>            <chr>               <int> <chr>         <chr>                         <int>      <int>
 #>  1 2e8c9911c9bfbf… 0ba16f4b-… 2e8c9911… 2e8c99… ""            <NA>             HDBR15279,HDBR1…       NA respiratory … cd14 mono                         1          1
@@ -497,7 +497,7 @@ Reading cpm â– â– â– â– â– â– â– â– â– â–
 
 single_cell_cpm
 #> # A SingleCellExperiment-tibble abstraction: 2,806 × 60
-#> # Features=1 | Cells=2806 | Assays=cpm
+#> # [90mFeatures=1 | Cells=2806 | Assays=cpm[0m
 #>    .cell observation_joinid dataset_id     sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA
 #>    <chr> <chr>              <chr>          <chr>     <chr>   <chr>         <chr>            <chr>               <int> <chr>                          <int>      <dbl>
 #>  1 80_1  zz-!e5_XAo         842c6f5d-4a94… 1de3f3ba… 1de3f3… ""            <NA>             7fabaf1c-52fd-4…    14600 breast                          1749      10.8 
@@ -769,7 +769,7 @@ get_metadata(
 #> ℹ Reading files.
 #> ℹ Compiling Experiment.
 #> # A SingleCellExperiment-tibble abstraction: 500 × 7
-#> # Features=13132 | Cells=500 | Assays=counts
+#> # [90mFeatures=13132 | Cells=500 | Assays=counts[0m
 #>    .cell            sample_id dataset_id cell_type_unified_ensemble atlas_id             file_id_cellNexus_single_cell         original_cell_
 #>    <chr>            <chr>     <chr>      <chr>                      <chr>                <chr>                                 <chr>         
 #>  1 AAACATACAACCAC_1 pbmc3k    pbmc3k     Memory CD4 T               cellxgene/03-10-2025 67e196a3c4e145151fc9e06c200e2f7f.h5ad AAACATACAACCAC

vignettes/cellNexus.Rmd.orig

@@ -83,7 +83,7 @@ suppressPackageStartupMessages({
 ### Load the metadata
 By default, `get_metadata()` loads harmonised annotations. Metadata is saved to `get_default_cache_dir()` unless a custom path is provided via the cache_directory argument. The `metadata` variable can then be re-used for all subsequent queries. 
 
-The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21388944/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21388944](https://zenodo.org/records/21388944).
+The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21633607/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21633607](https://zenodo.org/records/21633607).
 
 The following sections demonstrate the metadata, quality control, generation of raw and normalised counts, and pseudobulk construction for the specified query.
 

vignettes/gene-expression-explore.Rmd

@@ -11,7 +11,7 @@ vignette: >
 
 # Overview
 
-The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21388944/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21388944](https://zenodo.org/records/21388944).
+The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21633607/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21633607](https://zenodo.org/records/21633607).
 
 This page focuses on expression-layer retrieval workflows after metadata filtering. 
 

vignettes/gene-expression-explore.Rmd.orig

@@ -13,7 +13,7 @@ knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
 
 # Overview
 
-The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21388944/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21388944](https://zenodo.org/records/21388944).
+The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21633607/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21633607](https://zenodo.org/records/21633607).
 
 This page focuses on expression-layer retrieval workflows after metadata filtering.