1.6.9

PF2-pasteur-fr · Jul 10, 2019 · 6150a86 · 6150a86
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,12 +2,13 @@ Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
 Version: 1.6.9
-Date: 2019-06-14
+Date: 2019-07-10
 Author: Marie-Agnes Dillies and Hugo Varet
 Maintainer: Hugo Varet <[email protected]>
 Depends: R (>= 3.3.0), DESeq2 (>= 1.12.0), edgeR (>= 3.12.0), xtable
 Imports: stats, utils, graphics, grDevices, knitr, rmarkdown (>= 1.4), SummarizedExperiment, S4Vectors, limma, genefilter (>= 1.44.0)
 Suggests: optparse
+biocViews: Software
 VignetteBuilder: knitr, rmarkdown
 Encoding: latin1
 Description: Provide R tools and an environment for the statistical analysis of RNA-Seq projects: load and clean data, produce figures, perform statistical analysis/testing with DESeq2 or edgeR, export results and create final report.

diff --git a/NEWS b/NEWS
@@ -2,6 +2,7 @@ CHANGES IN VERSION 1.6.9
 ------------------------
 	o new vignette style
 	o print duplicated feature ids alongwith the error message in loadCountData()
+	o README update as Bioconductor dependencies are now automatically installed
 
 CHANGES IN VERSION 1.6.8
 ------------------------

diff --git a/R/loadCountData.R b/R/loadCountData.R
@@ -38,7 +38,7 @@ loadCountData <- function(target, rawDir="raw", skip=0, featuresToRemove=c("alig
   colnames(rawCounts) <- c("Id", labels[1])
   if (any(duplicated(rawCounts$Id))){
     stop("Duplicated feature names in ", files[1], ": ", 
-         unique(paste(rawCounts$Id[duplicated(rawCounts$Id)], collapse=", ")))
+         paste(unique(rawCounts$Id[duplicated(rawCounts$Id)]), collapse=", "))
   }
   cat("Loading files:\n")
   cat(files[1],": ",length(rawCounts[,labels[1]])," rows and ",sum(rawCounts[,labels[1]]==0)," null count(s)\n",sep="")
@@ -49,7 +49,7 @@ loadCountData <- function(target, rawDir="raw", skip=0, featuresToRemove=c("alig
     colnames(tmp) <- c("Id", labels[i])
     if (any(duplicated(tmp$Id))){
       stop("Duplicated feature names in ", files[i], ": ", 
-           unique(paste(tmp$Id[duplicated(tmp$Id)], collapse=", ")))
+           paste(unique(tmp$Id[duplicated(tmp$Id)]), collapse=", "))
     }
     rawCounts <- merge(rawCounts, tmp, by="Id", all=TRUE)
     cat(files[i],": ",length(tmp[,labels[i]])," rows and ",sum(tmp[,labels[i]]==0)," null count(s)\n",sep="")

diff --git a/README.md b/README.md
@@ -13,16 +13,15 @@ How to install SARTools?
 In addition to the SARTools package itself, the workflow requires the installation of several packages: DESeq2, edgeR, genefilter, xtable and knitr (all available online, see the dedicated webpages). SARTools needs R version 3.3.0 or higher, DESeq2 1.12.0 or higher and edgeR 3.12.0 or higher: old versions of DESeq2 or edgeR may be incompatible with SARTools.
 
 To install the SARTools package from GitHub, open a R session and:
-- install DESeq2, edgeR and genefilter with `if (!requireNamespace("BiocManager")){install.packages("BiocManager")}` and `BiocManager::install(c("DESeq2", "edgeR", "genefilter"))` (if not installed yet)
-- install devtools with `install.packages("devtools")` (if not installed yet)
+- Install devtools with `install.packages("devtools")` (if not installed yet)
 - Notes:
 
 	- Ubuntu users may have to install some libraries (libxml2-dev, libcurl4-openssl-dev and libssl-dev) to be able to install DESeq2 and devtools
 	- Some users may have to install the pandoc and pandoc-citeproc libraries to be able to generate the final HTML reports
 
-- for Windows users only, install [Rtools](https://cran.r-project.org/bin/windows/Rtools/) or check that it is already installed (needed to build the package)
-- load the devtools R package with `library(devtools)`
-- run `install_github("PF2-pasteur-fr/SARTools", build_opts="--no-resave-data")`
+- For Windows users only, install [Rtools](https://cran.r-project.org/bin/windows/Rtools/) or check that it is already installed (needed to build the package)
+- Load the devtools R package with `library(devtools)`
+- Run `install_github("PF2-pasteur-fr/SARTools", build_opts="--no-resave-data")`
 
 ### Using Conda
 

diff --git a/vignettes/SARTools.rmd b/vignettes/SARTools.rmd
@@ -216,25 +216,24 @@ The user can try the R scripts `template_script_DESeq2.r` and `template_script_e
 
 ## Bibliography
 
-[1] Anders S, Huber W. **Differential expression analysis for sequence count data**. *Genome Biology*. 2010; doi:10.1186/gb-2010-11-10-r106.
+[1] Anders S, Huber W. **Differential expression analysis for sequence count data**. *Genome Biology*. 2010.
 
-[2] Love M, Huber W, Anders S. **Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2**. *Genome Biology*. 2014; doi:10.1186/s13059-014-0550-8.
+[2] Love M, Huber W, Anders S. **Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2**. *Genome Biology*. 2014.
 
-[3] Robinson M, McCarthy DJ, Smyth GK. **edgeR: a Bioconductor package for differential expression analysis of digital gene expression data**. *Bioinformatics*. 2009; doi:10.1093/bioinformatics/btp616.
+[3] Robinson M, McCarthy DJ, Smyth GK. **edgeR: a Bioconductor package for differential expression analysis of digital gene expression data**. *Bioinformatics*. 2009.
 
-[4] Anders S, Pyl TP, Huber W. **HTSeq - A Python framework to work with high-throughput sequencing data**. *Bioinformatics*. 2014; doi:10.1093/bioinformatics/btu638.
+[4] Anders S, Pyl TP, Huber W. **HTSeq - A Python framework to work with high-throughput sequencing data**. *Bioinformatics*. 2014.
 
-[5] Liao Y, Smyth GK and Shi W. **featureCounts: an efficient general purpose program for assigning sequence reads to genomic features**. *Bioinformatics*, 2014; doi:10.1093/bioinformatics/btt656.
+[5] Liao Y, Smyth GK and Shi W. **featureCounts: an efficient general purpose program for assigning sequence reads to genomic features**. *Bioinformatics*, 2014.
 
-[6] Ritchie ME, Phipson B, Wu D, et al. **limma powers differential expression analyses for RNA-sequencing and microarray studies**. *Nucleic Acids Research*. 2015; doi:10.1093/nar/gkv007.
+[6] Ritchie ME, Phipson B, Wu D, et al. **limma powers differential expression analyses for RNA-sequencing and microarray studies**. *Nucleic Acids Research*. 2015.
 
-[7] Cook RD. **Detection of Influential Observation in Linear Regression**. *Technometrics*. 1977; DOI:10.1080/00401706.2000.10485981.
+[7] Cook RD. **Detection of Influential Observation in Linear Regression**. *Technometrics*. 1977.
 
-[8] Bourgon R, Gentleman R and Huber W. **Independent filtering increases detection power for high-throughput experiments**. *PNAS*. 2010; doi:10.1073/pnas.0914005107.
+[8] Bourgon R, Gentleman R and Huber W. **Independent filtering increases detection power for high-throughput experiments**. *PNAS*. 2010.
 
-[9] Benjamini Y and Hochberg Y. **Controlling the false discovery rate: a practical and powerful approach to multiple testing**. *Journal of the Royal Statistical Society B*. 1995; doi:10.2307/2346101.
+[9] Benjamini Y and Hochberg Y. **Controlling the false discovery rate: a practical and powerful approach to multiple testing**. *Journal of the Royal Statistical Society B*. 1995.
 
 [10] Benjamini Y and Yekutieli D. **The control of the false discovery rate in multiple testing under dependency**. *Annals of Statistics*. 2001.
 
-[11] Schulze SK, Kanwar R, Golzenleuchter M, et al. **SERE: Single-parameter quality control and sample comparison for RNA-Seq**. *BMC Genomics*. 2012; doi:10.1186/1471-2164-13-524.
-
+[11] Schulze SK, Kanwar R, Golzenleuchter M, et al. **SERE: Single-parameter quality control and sample comparison for RNA-Seq**. *BMC Genomics*. 2012.