Repositories list

• CAMPAREE

  Public
  Configurable And Modular Program Allowing RNA Expression Emulation

  Python

  •

  GNU General Public License v3.0

  •2•8•5•0•Updated Oct 23, 2025Oct 23, 2025

• dependent_sim_paper

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Oct 6, 2025Oct 6, 2025

• BEERS2

  Public
  Python

  •

  GNU General Public License v3.0

  •2•10•5•3•Updated Mar 31, 2025Mar 31, 2025

• BEERS_UTILS

  Public
  Utilities for the BEERS 2 suite of tools.

  Python

  •

  GNU General Public License v3.0

  •0•0•0•1•Updated Mar 31, 2025Mar 31, 2025

• Normalization

  Public
  RNA-Seq normalization and quantification pipeline

  Roff

  •

  GNU General Public License v3.0

  •6•12•6•0•Updated Nov 25, 2024Nov 25, 2024

• ITMAT_office_houRs

  Public
  0•1•0•0•Updated Jun 4, 2024Jun 4, 2024

• OmicsBenchmarkReport

  Public
  Report template for omics methods benchmarking

  Creative Commons Zero v1.0 Universal

  •0•1•0•0•Updated Oct 5, 2023Oct 5, 2023

• Barrel

  Public
  Python

  •0•0•0•0•Updated Aug 29, 2023Aug 29, 2023

• nitecap

  Public
  Nitecap is an exploratory circadian data analysis tool aimed at high-throughput omics data. It provides a web-interface to examine your dataset with highly-responsive visualizations, allowing the easy viewing of hundreds or thousands of genes or other features. Nitecap computes some standard rhythmicity tests for you, including JTK, ARSER, Lomb…

  HTML

  •

  GNU General Public License v3.0

  •1•3•0•4•Updated Feb 16, 2023Feb 16, 2023

• rum

  Public
  RNA-Seq Unified Mapper

  Roff

  •

  MIT License

  •4•26•49•1•Updated Sep 9, 2022Sep 9, 2022

• VODKA

  Public
  Perl

  •2•3•0•0•Updated Aug 23, 2020Aug 23, 2020

• chronobiome

  Public
  Adding additional datasets to Amy's chronobiome analyses

  R

  •

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

  •2•1•0•0•Updated Jan 29, 2019Jan 29, 2019

• DRINC

  Public
  Duplication Rate Identifier for NGS Cleanup

  Python

  •0•0•0•0•Updated Dec 3, 2018Dec 3, 2018

• DECAF

  Public
  Perl

  •0•0•0•0•Updated Apr 19, 2017Apr 19, 2017

• beers_simulator

  Public
  Perl

  •2•5•1•0•Updated Dec 29, 2015Dec 29, 2015

• bp1

  Public
  PHP

  •0•0•0•0•Updated Dec 17, 2015Dec 17, 2015

• AnovaSplice

  Public
  0•0•0•0•Updated Aug 14, 2015Aug 14, 2015

• bp2

  Public
  PHP

  •0•0•0•0•Updated Jun 12, 2015Jun 12, 2015

• isatab-templates

  Public
  ISATAB XML templates for use in ISACreator

  0•0•0•0•Updated Sep 18, 2014Sep 18, 2014

• pade

  Public
  Patterns from Gene Expression

  Python

  •

  Other

  •3•2•2•0•Updated Aug 29, 2014Aug 29, 2014

• collos

  Public
  CollOS : Collection Of Samples - a lightweight biobanking tool

  Ruby

  •1•0•0•0•Updated Mar 31, 2014Mar 31, 2014

• pre-pade

  Public
  Pre-PADE

  C

  •0•0•2•0•Updated Nov 7, 2013Nov 7, 2013

• itmat_archive

  Public
  Simple Rails application to archive the metadata of old experiments (which are on a bunch of disks)

  Ruby

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Aug 3, 2013Aug 3, 2013

• isareport

  Public
  ISA-Report: Makes nice looking HTML reports from ISA-TAB annotated experiments

  Python

  •0•0•0•0•Updated Apr 8, 2013Apr 8, 2013

• hogenesch-lab-website

  Public
  Hogenesch Lab Website

  PHP

  •1•2•0•0•Updated Apr 1, 2013Apr 1, 2013

• biopy-isatab

  Public
  Python parser for ISAtab, a biological file format for experimental metadata

  Python

  •3•0•0•0•Updated Aug 7, 2012Aug 7, 2012

• aspirin_analysis

  Public
  Aspirin Data Analysis on RoR

  Ruby

  •3•1•0•0•Updated Aug 1, 2012Aug 1, 2012

• bio-cookbooks

  Public
  A Chef cookbooks repository for bioinformatics tools

  Ruby

  •0•8•0•0•Updated Jan 20, 2012Jan 20, 2012

• pgfi-hts

  Public
  PGFI High Throughput Sequence Center Repo

  0•2•0•0•Updated Jun 27, 2011Jun 27, 2011

• chef-cookbooks

  Public
  Chef cookbooks for various services not directly related to bioinformatics, but are related to it

  Ruby

  •0•2•0•0•Updated May 5, 2011May 5, 2011