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

    TeX GPL-3.0 Updated Aug 9, 2018
  • TF Motif Variant Analysis

    Python Updated Aug 4, 2018
  • Prediction of Active Enhancers and Promoters in a Cell type specific manner using shape matching of histone and/or DNase-I hypersensitivity profiles

    Python 2 Updated Aug 3, 2018
  • SigLASSO: a LASSO approach jointly optimizing sampling likelihood and cancer mutation signatures

    R 1 Updated Jul 26, 2018
  • MUltiScale enrIchment Calling for ChIP-Seq Datasets

    C++ 16 Updated Jul 15, 2018
  • TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data

    Makefile Updated Jun 22, 2018
  • RADAR source code

    Python Updated May 14, 2018
  • Matlab Updated May 6, 2018
  • Python 1 Updated Apr 3, 2018
  • Output files and source code for our project predicting functional upstream open reading frames.

    Python 1 Updated Mar 28, 2018
  • Gerstein Lab Personal Page

    HTML 1 Updated Mar 28, 2018
  • Go Updated Mar 22, 2018
  • Software for preprocessing, filtering, alignment, and reporting of smallRNA-seq datasets

    Java 2 7 GPL-3.0 Updated Mar 19, 2018
  • Spectral and reproducibility analysis of Hi-C contact maps

    Julia 6 3 Updated Feb 18, 2018
  • 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.

    C++ Updated Jan 31, 2018
  • Negative binomial regression fitting code in C++. Adapted from R source code.

    C++ Updated Jan 31, 2018
  • Mutations Overburdening Annotations Tool

    C++ Updated Dec 4, 2017
  • C 3 2 Updated Oct 4, 2017
  • Julia 4 6 Updated Apr 27, 2017
  • a method to identify TADs in Hi-C data

    Julia 4 2 Updated Apr 26, 2017
  • An integrated retroduplication caller based on 1) exon-exon junction and 2) discordant reads

    Perl 1 Updated Apr 20, 2017
  • A flexible framework to annotate and prioritize cancer somatic mutations.

    Perl 3 3 CC0-1.0 Updated Apr 18, 2017
  • 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…

    Perl 2 Updated Oct 29, 2016
  • 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.

    Python 2 Updated Aug 28, 2016
  • Python 1 GPL-3.0 Updated Aug 16, 2016
  • Large-scale Analysis of Recurrent Variants in noncoding Annotations

    C++ 2 1 Updated Aug 9, 2016
  • Server code for STRESS

    C Updated Aug 3, 2016
  • Identifying and ranking peak regions in ChIP-Seq experiments

    C++ 1 Updated Mar 23, 2016
  • Moving big files around the network

    Python Updated Jun 13, 2015
  • Updated Jun 9, 2015