Grow your team on GitHub
GitHub is home to over 28 million developers working together. Join them to grow your own development teams, manage permissions, and collaborate on projects.Sign up
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.
The package includes the MotifVar pipeline developed in the Gerstein Lab at Yale for the Intensification resource. This pipeline was used to generate SNV population-genetic profiles using a variety of public data sources, including SMART domain database, ExAC, Ensembl and VEP. Please see website for more detailed README. This is a SEMI-automated…
The package includes the AlleleDB pipeline developed in the Gerstein Lab at Yale. This pipeline was built and applied to perform a uniform identification of SNVs associated with allele-specific binding and expression in 382 individuals from the 1000 Genomes Project. Please see website for more detailed README.
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