| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
Package: GSVA |
| 2 |
-Version: 1.27.2 |
|
| 2 |
+Version: 1.27.3 |
|
| 3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
| 4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
|
| 5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
|
| ... | ... |
@@ -26,7 +26,7 @@ setMethod("gsva", signature(expr="ExpressionSet", gset.idx.list="list"),
|
| 26 | 26 |
sdGenes <- Biobase::esApply(expr, 1, sd) |
| 27 | 27 |
if (any(sdGenes == 0) || any(is.na(sdGenes))) {
|
| 28 | 28 |
warning(sum(sdGenes == 0 | is.na(sdGenes)), |
| 29 |
- "genes with constant expression values throuhgout the samples.") |
|
| 29 |
+ " genes with constant expression values throuhgout the samples.") |
|
| 30 | 30 |
if (method != "ssgsea") {
|
| 31 | 31 |
warning("Since argument method!=\"ssgsea\", genes with constant expression values are discarded.")
|
| 32 | 32 |
expr <- expr[sdGenes > 0 & !is.na(sdGenes), ] |
| ... | ... |
@@ -93,7 +93,7 @@ setMethod("gsva", signature(expr="ExpressionSet", gset.idx.list="GeneSetCollecti
|
| 93 | 93 |
sdGenes <- Biobase::esApply(expr, 1, sd) |
| 94 | 94 |
if (any(sdGenes == 0) || any(is.na(sdGenes))) {
|
| 95 | 95 |
warning(sum(sdGenes == 0 | is.na(sdGenes)), |
| 96 |
- "genes with constant expression values throuhgout the samples.") |
|
| 96 |
+ " genes with constant expression values throuhgout the samples.") |
|
| 97 | 97 |
if (method != "ssgsea") {
|
| 98 | 98 |
warning("Since argument method!=\"ssgsea\", genes with constant expression values are discarded.")
|
| 99 | 99 |
expr <- expr[sdGenes > 0 & !is.na(sdGenes), ] |
| ... | ... |
@@ -164,7 +164,7 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="GeneSetCollection"),
|
| 164 | 164 |
sdGenes <- apply(expr, 1, sd) |
| 165 | 165 |
if (any(sdGenes == 0) || any(is.na(sdGenes))) {
|
| 166 | 166 |
warning(sum(sdGenes == 0 | is.na(sdGenes)), |
| 167 |
- "genes with constant expression values throuhgout the samples.") |
|
| 167 |
+ " genes with constant expression values throuhgout the samples.") |
|
| 168 | 168 |
if (method != "ssgsea") {
|
| 169 | 169 |
warning("Since argument method!=\"ssgsea\", genes with constant expression values are discarded.")
|
| 170 | 170 |
expr <- expr[sdGenes > 0 & !is.na(sdGenes), , drop=FALSE] |
| ... | ... |
@@ -237,7 +237,7 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="list"),
|
| 237 | 237 |
sdGenes <- apply(expr, 1, sd) |
| 238 | 238 |
if (any(sdGenes == 0) || any(is.na(sdGenes))) {
|
| 239 | 239 |
warning(sum(sdGenes == 0 | is.na(sdGenes)), |
| 240 |
- "genes with constant expression values throuhgout the samples.") |
|
| 240 |
+ " genes with constant expression values throuhgout the samples.") |
|
| 241 | 241 |
if (method != "ssgsea") {
|
| 242 | 242 |
warning("Since argument method!=\"ssgsea\", genes with constant expression values are discarded.")
|
| 243 | 243 |
expr <- expr[sdGenes > 0 & !is.na(sdGenes), , drop=FALSE] |
| ... | ... |
@@ -4,6 +4,7 @@ |
| 4 | 4 |
[](http://bioconductor.org/packages/stats/bioc/GSVA.html "Percentile (top 5/20/50% or 'available') of downloads over the last 6 full months") |
| 5 | 5 |
[](http://bioconductor.org/packages/devel/bioc/html/GSVA.html#svn_source "Average SVN commits (to the devel branch) per month over the last 6 months") |
| 6 | 6 |
[](https://support.bioconductor.org/t/GSVA/ "Bioconductor support site activity on GSVA, last 6 months: tagged questions/avg. answers per question/avg. comments per question/accepted answers, or 0 if no tagged posts.") |
| 7 |
+<img align="right" src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/GSVA/GSVA.png" height="200"/> |
|
| 7 | 8 |
|
| 8 | 9 |
**Current build status** |
| 9 | 10 |
- `release` [](http://bioconductor.org/packages/release/bioc/html/GSVA.html#archives "Whether GSVA release is available on all platforms") |
| ... | ... |
@@ -11,6 +12,10 @@ |
| 11 | 12 |
- `development` [](http://bioconductor.org/packages/devel/bioc/html/GSVA.html#archives "Whether GSVA devel is available on all platforms") |
| 12 | 13 |
[](http://bioconductor.org/checkResults/devel/bioc-LATEST/GSVA/ "Bioconductor devel build") |
| 13 | 14 |
|
| 15 |
+The `GSVA` package allows one to perform a change in coordinate systems of molecular measurements, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. For citing `GSVA` as a software package, please use the following reference: |
|
| 16 |
+ |
|
| 17 |
+ Hänzelmann S., Castelo R. and Guinney J. GSVA: gene set variation analysis for microarray and RNA-Seq data. BMC _Bioinformatics_, 14:7, 2013. |
|
| 18 |
+ |
|
| 14 | 19 |
## Installation |
| 15 | 20 |
|
| 16 | 21 |
This is the __development__ version of the R/Bioconductor package GSVA. This version is unstable and should be used only to test new features. If you are looking for the __release__ version of this package please go to its package release landing page at [http://bioconductor.org/packages/GSVA](http://bioconductor.org/packages/GSVA) and follow the instructions there to install it. |
