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Software

A list of available software packages. Please also check out https://github.com/ratschlab.

Folder SHOGUN
Large-scale Machine Learning Toolbox
Folder PALMapper
RNA-Seq short read aligner program
Folder mGene
A computational tool for accurate genome-wide prediction of genes from DNA sequences
Folder rQuant
A tool for transcriptome quantitation from RNA-seq experiments
Folder KIRMES
Kernel-based Identification of Regulatory Modules in Euchromatic Sequences
Folder EasySVM
A set of tools based on the Shogun toolbox allowing to train and test SVMs in a simple way
Folder ARTS
A tool for Accurate Recognition of Transcription Starts in Human
Folder ASP
A program to predict accurate splice sites on genomic sequences of several organisms
Folder QPALMA
Aligning spliced reads produced by Next generation sequencing technologies
Folder MiTie
Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples
Folder rDiff : Accurate Detection of Differential RNA Processing
Supplemental Material for the Manuscript "Accurate Detection of Differential RNA Processing" by Philipp Drewe, Oliver Stegle, Lisa Hartmann, Andre, Kahles, Regina Bohnert, Andreas Wachter, Karsten Borgward, and Gunnar Rätsch
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