Gerstein Lab

TF Motif Variant Analysis

CBB752 SP2019 Course Website

Server code for STRESS

#DSPN

RADAR source code

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

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

ALOFT, the Annotation Of Loss-of-Function Transcripts, provides extensive functional annotations to loss-of-function variants in the human genome.

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

Using sliding window to extract k-mers for annotation (specfically exons) in GTF format

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

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