bubhub/mrnaseq repository overview

This image contains a core set of software the Hub uses in RNA-Seq analysis. It is based off of the python:3.6-stretch base image. Packages installed:

Software packages:

• bedtools v2.27.1
• bowtie v1.2.2
• bowtie2 v2.3.4.2
• bwa v0.7.17
• cutadapt v1.17
• de_toolkit v0.6.0
• DNApi (https://github.com/jnktsj/DNApi⁠)
• fastqc v0.11.7
• fastxtoolkit v0.0.13
• kallisto v0.44.0
• multiqc v1.6
• salmon v0.11.1
• samtools v1.9
• STAR v2.6.0c
• trimmomatic v0.38
• verse v0.1.5
• R v3.3.3

R packages:

• jsonlite
• logistf
• DESeq2 (bioconductor)

python packages:

• pysam