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: wangdp123@gmail.com)
Thanks,
Dapeng
do you have something against github or even bitbucket? sourceforge is a ghost town