Tools

CLIP data processing

We provide a complete workflow for the processing of CLIP data and the tool racoon_clip, which automatises this workflow.

A bioinformatics pipeline for iCLIP data analysis

iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites

racoon_clip - complete CLIP processing from one single command

racoon processes your raw iCLIP or eCLIP read data to crosslinks with single nucleotide resolution.

R/Bioconductor software packages

We contribute to the Bioconductor project with the following tools …

BindingSiteFinder

An R/ Bioconductor software package for RBP binding site definition

Differential binding

A BindingSiteFinder R/ Bioconductor software extention for RBP binding site regulation

cliProfiler

An easy and fast way to visualize and profile the high-throughput IP data. This package generates the meta gene profile and other profiles. These profiles could provide…

m6Aboost

This package can help user to run the m6Aboost model on their own miCLIP2 data. The package includes functions to assign the read counts and get the features to run the…

circRNAs

We provide a commandline application for the detection of circular RNAs.

Calcifer: A workflow for circRNA detection and analysis

Calcifer is a workflow for highly automated detection and analysis of circRNAs in RNA-Seq datasets.