Repositories list

• lncRNARN

  Public
  Script, code and data for analyses in the paper "Quantitative estimates of the regulatory influence of long non-coding RNAs on global gene expression variation using TCGA breast cancer transcriptomic data".

  R

  •0•1•0•0•Updated Jan 29, 2024Jan 29, 2024

• VarSAn

  Public
  R

  •1•2•0•0•Updated Oct 10, 2023Oct 10, 2023

• GEMSTAT

  Public
  Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression

  C++

  •8•6•27•0•Updated Jun 8, 2022Jun 8, 2022

• Stubb

  Public
  0•0•0•0•Updated Dec 23, 2021Dec 23, 2021

• phyme

  Public
  0•0•0•0•Updated Dec 23, 2021Dec 23, 2021

• cisMetalysis

  Public
  0•0•0•0•Updated Dec 23, 2021Dec 23, 2021

• crmfinding

  Public
  0•0•0•0•Updated Dec 23, 2021Dec 23, 2021

• d2z

  Public
  0•0•0•0•Updated Dec 23, 2021Dec 23, 2021

• dips

  Public
  0•0•0•0•Updated Dec 23, 2021Dec 23, 2021

• EvolSimul

  Public
  0•0•0•0•Updated Dec 23, 2021Dec 23, 2021

• gemstat-gl

  Public
  HTML

  •0•0•0•0•Updated Dec 23, 2021Dec 23, 2021

• indelign

  Public
  0•0•0•0•Updated Dec 23, 2021Dec 23, 2021

• SCRMshaw

  Public
  0•0•0•0•Updated Dec 23, 2021Dec 23, 2021

• stemma

  Public
  0•0•0•0•Updated Dec 22, 2021Dec 22, 2021

• swan

  Public
  0•0•0•0•Updated Dec 22, 2021Dec 22, 2021

• GEMSTAT_scripts

  Public
  Various task-agnostic scripting language tools for dealing with GEMSTAT.

  Python

  •1•0•1•0•Updated Oct 15, 2021Oct 15, 2021

• GEMSTAT_refinement_sampler

  Public
  A tool to allow meaningful comparison of different refinement methods for GEMSTAT models.

  Shell

  •1•1•8•0•Updated May 22, 2020May 22, 2020

• SERGIO

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 24, 2019Oct 24, 2019

• Enhancer-Activity-Predictor

  Public
  R

  •0•1•0•0•Updated Sep 26, 2019Sep 26, 2019

• MOP

  Public
  C++

  •0•0•0•0•Updated May 1, 2019May 1, 2019

• Lab-Docker

  Public
  Docker Containers used in the lab

  Dockerfile

  •1•0•0•0•Updated Oct 17, 2018Oct 17, 2018

• autotools-unittest

  Public
  The autotools-unittest is a minimal starter kit when writing C++ library with autotools, google test and google mock.

  C++

  •

  BSD 3-Clause "New" or "Revised" License

  •6•0•0•0•Updated May 25, 2018May 25, 2018

• SNOT_lang

  Public
  Simple Numerical Object Transcription (SNOT) is a language similar to JSON meant for numerical computing.

  C++

  •

  MIT License

  •1•0•0•0•Updated Nov 15, 2017Nov 15, 2017

• ASTER

  Public
  Analysis of SNPs Targeting Evolutionary Rates

  0•0•0•0•Updated Jul 12, 2017Jul 12, 2017

• STAP

  Public
  A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data. http://www.ncbi.nlm.nih.gov/pubmed/19956545

  C++

  •0•1•0•0•Updated Apr 9, 2015Apr 9, 2015

• CPPExperiments

  Public
  A cannonical place to store C++ example code / experiments that will allow us to pin down certain behaviours. Then we can approach our other projects with confidence.

  C++

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Apr 2, 2015Apr 2, 2015

• linuxbrew

  Public
  A fork of Homebrew for Linux

  Ruby

  •

  Other

  •296•0•0•0•Updated Jan 23, 2015Jan 23, 2015

• SinhaLab_Infrastructure

  Public
  Workaround because we have an ancient Linux distribution

  Shell

  •0•0•0•0•Updated Jan 22, 2015Jan 22, 2015