diff --git a/DESCRIPTION b/DESCRIPTION
index d2dc29d..38a21a3 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,9 +1,10 @@
 Package: arkas
 Type: Package
 Title: A package that complements Kallisto for quick, informative *seq analysis
-Version: 0.44.9
-Date: 2016-08-13
+Version: 0.98.0
+Date: 2016-08-26
 Author: Tim Triche, Jr., Anthony Colombo, Harold Pimentel
+biocViews: RNASeq, Transcriptomics
 Depends:
     SummarizedExperiment,
     tools
@@ -28,7 +29,13 @@ Imports:
     GenomeInfoDb,
     methods,
     S4Vectors,
-    GenomicFeatures
+    GenomicFeatures,
+    grDevices, 
+    graphics, 
+    grid, 
+    parallel, 
+    stats,
+    utils
 Suggests:
     knitr,
     roxygen2,
diff --git a/NAMESPACE b/NAMESPACE
index 71b0979..4a137ab 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -64,6 +64,8 @@ importFrom(IRanges,reduce)
 importFrom(RUVSeq,RUVg)
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,metadata)
+importFrom(S4Vectors,queryHits)
+importFrom(S4Vectors,subjectHits)
 importFrom(TxDbLite,createAnnotationPackage)
 importFrom(TxDbLite,findDupes)
 importFrom(TxDbLite,getAnnotationType)
diff --git a/R/collapseByTss.R b/R/collapseByTss.R
index bbd319f..d0a657b 100644
--- a/R/collapseByTss.R
+++ b/R/collapseByTss.R
@@ -7,6 +7,8 @@
 #' @return  the TSS for transcripts on chr1:22/X/Y/M to collapse by TSS,
 #'          or NA for transcripts originating anywhere else (ERCC, repeats, &c)
 #'
+#' @importFrom S4Vectors queryHits 
+#' @importFrom S4Vectors subjectHits 
 #' @importFrom GenomeInfoDb seqlevels
 #' @importFrom GenomeInfoDb seqlevelsStyle
 #' @importFrom GenomeInfoDb seqlevelsInGroup seqnames
diff --git a/R/extractIndexName.R b/R/extractIndexName.R
index 8daa8b5..2d372f6 100755
--- a/R/extractIndexName.R
+++ b/R/extractIndexName.R
@@ -8,6 +8,6 @@
 extractIndexName <- function(callinfo) {
   pop <- function(x) x[length(x)] 
   popsplit <- function(x, y=.Platform$file.sep) pop(strsplit(x, y)[[1]])
-  tokens <- strsplit(callinfo, " ", fixed=T)[[1]]
+  tokens <- strsplit(callinfo, " ", fixed=TRUE)[[1]]
   popsplit(tokens[grep("^-i$", tokens) + 1])
 }