• Software
• single cell RNA-seq preprocessing
• cERMIT
• Cseq-Simulator
• DeepRiPe
• FootprintMixture
• Reproducible footprinting
• FootprintPipeline
• JACUSA
• JAMM Peak Finder
• MUMMIE
• microMUMMIE
• Intro to Multivariate Markov Modeling
• microMUMMIE Drosophila
• McEnhancer
• NASTIseq
• omniCLIP
• Orthologous Enhancers
• 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

Software

List of software from the Lab

This site largely contains legacy tools.
Note that recent code (2020-) can be found at our github repository.

Prediction of coding and non-coding genes:

NASTISeq

PIPmiR

RNAmetabolism

RSVP

Promoter and enhancer analysis:

Orthologous Enhancers

S-Peaker

McEnhancer

TF target site identification:

FootprintMixture

FootprintPipeline

ChIP/CLIP analysis:

cERMIT

Crosslinked-sequence (Cseq) Simulator

JAMM

PARalyzer

miRNA target prediction:

MUMMIE

TargetThermo

Ribosome profiling:

RiboTaper

Regulatory network topology:

WaRSwap

Gene expression imaging:

Root_imaging_pipeline

Analysis of RNA-binding proteins: 

DeepRiPe

omniCLIP

ssHMM

SSMART

RCK

Identification of RNA editing events:

JACUSA

Best practice tools for sequencing:

The RNA workbench