• Software
• single cell RNA-seq preprocessing
• cERMIT
• Cseq-Simulator
• DeepRiPe
• FootprintMixture
• Reproducible footprinting
• FootprintPipeline
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• JAMM Peak Finder
• MUMMIE
• microMUMMIE
• Intro to Multivariate Markov Modeling
• microMUMMIE Drosophila
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• PARalyzer
• mEAT
• PARpipe
• PIPmiR
• RCK
• RNAmetabolism
• Data and Pipeline Download
• The RNA workbench
• RSVP
• RiboTaper
• Root_imaging_pipeline
• S-Peaker
• Supplementary Material
• Installation
• ssHMM
• SSMART
• TargetThermo
• WaRSwap

Cseq-Simulator (Crosslinked-sequence Simulator)

CSEQ-SIMULATOR: A DATA SIMULATOR FOR CLIP-SEQ EXPERIMENTS

Publication:

Kassuhn, W., Ohler. U., Drewe, P. (2016).  Cseq-Simulator: A data simulator dor CLIP-Seq experiments. Pac Symp Biocomput..

Abstract

Cseq-Simulator is a pipeline for realistic RNA-Clip simulations. It mimics key steps of Clip protocols and allows with user provided profiles to simulate any diagnostic event distribution (RBPs). Furthermore, Cseq-Simulator is very individual and lets the user provide a list of RBP binding sites or transcipt abundance profiles.

Requirements:
Flux-simulator
FIMO as part of MEME

Downloads:
Cseq-Simulator v1.02 (Documentation)
Cseq-Simulator v1.01  (Documentation)
Cseq-Simulator v1.00  (Documentation)