This repository has been marked as deprecated, so some tool shed features may be restricted.
Repository deseq_and_sam2counts
Name: deseq_and_sam2counts
Owner: nikhil-joshi
Synopsis: Performs RNA-Seq differential expression analysis on aligned reads to a transcriptome using sam2counts and DESeq 1.8.3
This is a Galaxy package that wraps sam2counts and DESeq for RNA-Seq analysis using a transcriptome reference.  sam2counts takes SAM or BAM files that are created from an alignment to a transcriptome and creates counts of aligned reads for each transcript.  DESeq uses the DESeq package (version 1.8.3) from Bioconductor in R and analyzes the count data from sam2counts. DESeq outputs a toptable of transcripts sorted by adjusted p-value and a page of diagnostic plots.
Link to this repository: https://toolshed.g2.bx.psu.edu/view/nikhil-joshi/deseq_and_sam2counts/a49aff09553e
Type: unrestricted
Revision: 3:a49aff09553e
This revision can be installed: True
Times cloned / installed: 317

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
Produce count data from SAM or BAM files 1.0.0 any
Run Differential Expression analysis from SAM To Count data 1.0.0 any

Categories
Next Gen Mappers - Tools for the analysis and handling of Next Gen sequencing data
SAM - Tools for manipulating alignments in the SAM format
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
Statistics - Tools for generating statistics
Visualization - Tools for visualizing data