Gerstein Lab

Repositories

• SVFX

  Machine learning framework to quantify pathogenicity of structural variants
  Python MIT 3 4 0 1 Updated Sep 8, 2020

• ThermoNet

  ThermoNet is a computational framework for quantitative prediction of the impact of single-point mutations on protein thermodynamic stability. The core algorithm of ThermoNet is an ensemble of deep 3D convolutional neural networks.
  Python GPL-3.0 2 10 0 0 Updated Sep 4, 2020

• Bay2Ctrls

  Bayesian model to integrate two types of ChIP-seq controls for binding site detection
  R 0 0 0 0 Updated Aug 26, 2020

• idash19he
  C++ 0 2 0 0 Updated Aug 25, 2020

• papers.gersteinlab.org
  Go 0 2 0 0 Updated Aug 10, 2020

• SAMChain
  Python 2 3 0 0 Updated Aug 7, 2020

• idash19bc

  Solution to iDASH'19 challenge track 1
  JavaScript 0 3 0 0 Updated Jul 27, 2020

• SCF
  R 0 0 0 0 Updated Jul 20, 2020

• siglasso

  Optimizing Cancer Mutation Signatures Jointly with Sampling Likelihood
  R 1 4 1 0 Updated Jul 17, 2020

• MOBI
  Jupyter Notebook 0 0 0 0 Updated Jul 16, 2020

• FANCY

  Predicting privacy risk of functional genomics data
  Jupyter Notebook 1 1 0 0 Updated May 28, 2020

• starrpeaker

  STARRPeaker: STARR-seq peak caller
  Python GPL-3.0 3 8 0 0 Updated May 20, 2020

• nimbus
  R 0 0 0 0 Updated May 16, 2020

• dAsthma
  R 0 0 0 0 Updated Apr 27, 2020

• decoasthma

  Code to reproduce the analyses described in the manuscript, "Approaches for integrating heterogeneous RNA-seq data reveals cross-talk between microbes and genes in asthmatic patients"
  HTML MIT 1 0 0 1 Updated Apr 27, 2020

• cbb752b20
  CSS 0 0 0 0 Updated Apr 15, 2020

• MrTADFinder

  a method to identify TADs in Hi-C data

  hi-c 3d-genome
  Julia 3 4 0 0 Updated Mar 28, 2020

• genetracer
  0 0 0 0 Updated Feb 28, 2020

• esprnn

  Forked from hoondy/esprnn

  ESPRNN: Epigenome-based Splicing Prediction using Recurrent Neural Network
  Python 1 0 0 0 Updated Feb 11, 2020

• idash19

  idash19 solutions
  JavaScript 0 0 0 0 Updated Dec 16, 2019

• topicnet
  R 0 2 0 0 Updated Nov 20, 2019

• aloft

  ALOFT, the Annotation Of Loss-of-Function Transcripts, provides extensive functional annotations to loss-of-function variants in the human genome.
  Python CC0-1.0 3 13 1 0 Updated Nov 4, 2019

• LESSeq

  Local Event-based analysis of alternative Splicing using RNA-Seq
  C MIT 0 7 3 0 Updated Nov 2, 2019

• texp

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

  bioinformatics bioinformatics-pipeline
  Makefile Apache-2.0 1 3 0 0 Updated Oct 10, 2019

• HotCommics
  C 0 0 0 0 Updated Sep 5, 2019

• Evotum101

  Modelling tumor progression from a single VCF file
  Perl 6 GPL-3.0 0 0 2 0 Updated Aug 22, 2019

• GRAM

  GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell type-specific manner
  R 1 0 0 0 Updated May 3, 2019

• HiC-spector

  Spectral and reproducibility analysis of Hi-C contact maps

  hi-c 3d-genome
  Julia 6 9 4 1 Updated May 1, 2019

• cbb752b19

  CBB752 SP2019 Course Website
  CSS 0 0 0 0 Updated Apr 18, 2019

• MUSIC

  MUltiScale enrIchment Calling for ChIP-Seq Datasets
  C++ 0 22 2 0 Updated Mar 14, 2019