Gerstein Lab

flanking k-mer extractor will extract k-mers in the flanking regions of annotation specified in GTF format

TF Motif Variant Analysis

Prediction of Active Enhancers and Promoters in a Cell type specific manner using shape matching of histone and/or DNase-I hypersensitivity profiles

SigLASSO: a LASSO approach jointly optimizing sampling likelihood and cancer mutation signatures

MUltiScale enrIchment Calling for ChIP-Seq Datasets

TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data

RADAR source code

Output files and source code for our project predicting functional upstream open reading frames.

Gerstein Lab Personal Page

Software for preprocessing, filtering, alignment, and reporting of smallRNA-seq datasets

Spectral and reproducibility analysis of Hi-C contact maps

Logistic regression fitting code designed for use with CUDA. Rather than speeding up the running time of a single regression, the code performs the regression in parallel on hundreds of samples.

Negative binomial regression fitting code in C++. Adapted from R source code.

Mutations Overburdening Annotations Tool

a method to identify TADs in Hi-C data

An integrated retroduplication caller based on 1) exon-exon junction and 2) discordant reads

A flexible framework to annotate and prioritize cancer somatic mutations.

Large-scale Analysis of Recurrent Variants in noncoding Annotations

Server code for STRESS

Identifying and ranking peak regions in ChIP-Seq experiments

Moving big files around the network