skip to navigation
skip to content

Not Logged In

READemption 0.2.0

A RNA-Seq Analysis Pipeline

Package Documentation

Latest Version: 0.3.7

About

READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed at the IMIB/ZINF to process dRNA-Seq reads (as introduced by Sharma et al., Nature, 2010 originating from bacterial samples. Meanwhile is has been extended to process data generated in different experimental setups and originating from all domains of life and is under active development. The subcommands which are provided by command-line interface cover read processing and aligning, coverage plot generation, gene expression quantification as well as differential gene expression analysis. READemption was applied to analyze numerous data sets. In order to set up analyses quickly READemption follows the principal of “convention over configuration”: Once the input files are copied into defined folders no further parameters have to be given. Still, READemption’s behavior can be adapted to specific needs of the user.

License

ICSL - see LICENSE.txt

Development

  • If possible follow the principal of “convention over configuration”. This means input file are into a fixed location and the result file are placed in fixed location.

  • The classes should be path agnostic as far a possible. The controller is taking care of that and calls them adequately.

  • The git braching model is very close to the one proposed here. There two main branches:

    • master
    • dev(elopment)

    And there are further supporting branches:

    • feature branches - branched off and back to the dev branch
    • release branches - branched off from dev and merged back into dev and master
    • hotfix branches - branched off from master and merged back into dev and master
 
File Type Py Version Uploaded on Size
READemption-0.2.0.tar.gz (md5) Source 2014-03-30 36KB
  • Downloads (All Versions):
  • 38 downloads in the last day
  • 503 downloads in the last week
  • 1418 downloads in the last month