| This tool performs differential representation analysis on either a fastq file of sgRNA/shRNA sequencing reads or a table of counts specifying sgRNA/shRNA counts across multiple samples. There are options to use exact tests or generalised linear models, the latter allowing for gene set testing. The outputs contain a MDS plot, MA plot and a ranked table of hairpins in ascending p-value containing other statistics.
Tutorial for using this tool is available: http://bioinf.wehi.edu.au/shRNAseq/galaxy.html |
hg clone https://toolshed.g2.bx.psu.edu/repos/shians/shrnaseq