Software

SHOGUN

Large-scale Machine Learning Toolbox

PALMapper

RNA-Seq short read aligner program

mGene

A computational tool for accurate genome-wide prediction of genes from DNA sequences

rQuant

A tool for transcriptome quantitation from RNA-seq experiments

KIRMES

Kernel-based Identification of Regulatory Modules in Euchromatic Sequences

EasySVM

A set of tools based on the Shogun toolbox allowing to train and test SVMs in a simple way

ARTS

A tool for Accurate Recognition of Transcription Starts in Human

ASP

A program to predict accurate splice sites on genomic sequences of several organisms

QPALMA

Aligning spliced reads produced by Next generation sequencing technologies

MiTie

Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples

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