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Source: rockhopper
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>,
Pierre Gruet <pgt@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
imagemagick,
javahelper,
default-jdk,
igv
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/rockhopper
Vcs-Git: https://salsa.debian.org/med-team/rockhopper.git
Homepage: https://cs.wellesley.edu/~btjaden/Rockhopper/
Rules-Requires-Root: no
Package: rockhopper
Architecture: all
Depends: ${misc:Depends},
${java:Depends},
default-jre
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
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