hppRNA: a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis

[wangdp]

Hi there,

I am delighted to announce the release of a new comprehensive pipeline for RNA-Seq analysis on local server - hppRNA.

This tool integrates six workflows such as Tophat–Cufflink–Cuffdiff, Subread–featureCounts–DESeq2, STAR–RSEM–EBSeq, Bowtie–eXpress–edgeR, kallisto–sleuth, and HISAT–StringTie–Ballgown to handle fastq files and generate the gene expression matrix and differentially-expressed-genes.

In addition, it detects SNPs and fusion genes and copes with long noncoding RNAs and circular analysis.

The link to the package for downloading:

https://sourceforge.net/projects/hpprna/

Reference:

Dapeng Wang. hppRNA-a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples.. Brief Bioinform. 2017 Jan 17. pii: bbw143. doi: 10.1093/bib/bbw143.

https://www.ncbi.nlm.nih.gov/pubmed/28096075

Please let me know if you encounter any issues when using this pipeline. (email address: [email protected])

Thanks,

Dapeng