Bug#1005356: ITP: rockhopper -- system for analyzing bacterial RNA-seq data

[Andreas Tille <andreas@an3as.eu>]

Very cool!

Am Fri, Feb 11, 2022 at 10:08:25PM +0100 schrieb Pierre Gruet:
> Package: wnpp
> Severity: wishlist
> Owner: Debian-med team <debian-med@lists.debian.org>
> X-Debbugs-Cc: debian-devel@lists.debian.org, debian-med@lists.debian.org
> 
> * Package name    : rockhopper
>   Version         : 2.0.3
>   Upstream Author : Brian Tjaden
> * URL             : https://cs.wellesley.edu/~btjaden/Rockhopper
> * License         : GPL-3+
>   Programming Lang: Java
>   Description     : system for analyzing bacterial RNA-seq data
> 
> Rockhopper is a comprehensive and user-friendly system for
> computational analysis of bacterial RNA-seq data. As input, Rockhopper
> takes RNA sequencing reads output by high-throughput sequencing
> technology (FASTQ, QSEQ, FASTA, SAM, or BAM files). Rockhopper supports
> the following tasks:
> * Reference based transcript assembly (when one or more reference
>   genomes are available)
>   - Aligning reads to genomes
>   - Assembling transcripts
>   - Identifying transcript boundaries and novel transcripts such as
>     small RNAs
> * De novo transcript assembly (when reference genomes are unavailable)
> * Normalizing data from different experiments
> * Quantifying transcript abundance
> * Testing for differential gene expression
> * Characterizing operon structures
> * Visualizing results in a genome browser
> 
> The package will be team-maintained by Debian-med team.
> 
> 

-- 
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