Repositories list

• misc2

  Public
  misc is dead! long live the misc2

  Java

  •

  GNU Lesser General Public License v2.1

  •0•1•0•0•Updated Jul 31, 2025Jul 31, 2025

• gsplot

  Public
  Gene set viewer

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

• repo

  Public
  Repository for maven jars and other resources.

  0•0•0•0•Updated Jul 30, 2025Jul 30, 2025

• utility

  Public
  Contains code that is often shared by many projects.

  Java

  •2•1•0•3•Updated Jul 30, 2025Jul 30, 2025

• resource

  Public
  Collection of code for accessing several data resources.

  Java

  •

  GNU Lesser General Public License v3.0

  •1•0•1•3•Updated Jul 30, 2025Jul 30, 2025

• causalpath

  Public
  A project for exploring differentially active signaling paths related to proteomics datasets

  bioinformaticscomputational-biologyproteomics+ 4pathwaysphosphoproteomicscausality-analysispathway-analysis

  Java

  •

  GNU Lesser General Public License v3.0

  •11•43•6•2•Updated Jul 30, 2025Jul 30, 2025

• TF-PREDICTION-WEB

  Public
  Python

  •0•0•0•0•Updated Jul 29, 2025Jul 29, 2025

• causalpath-newt-webserver

  Public
  JavaScript

  •

  MIT License

  •1•1•6•0•Updated Jul 25, 2025Jul 25, 2025

• sbgnviz.js

  Public
  A web based visualization tool for process description maps in SBGN

  JavaScript

  •

  GNU Lesser General Public License v3.0

  •19•0•0•0•Updated Jul 25, 2025Jul 25, 2025

• TF-Analysis

  Public
  Jupyter Notebook

  •

  GNU Lesser General Public License v2.1

  •0•0•2•0•Updated Nov 13, 2024Nov 13, 2024

• RNAToProtein

  Public
  A linear regression framework for predicting proteomic values from transcriptomic data.

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 21, 2024Apr 21, 2024

• single-cell-pathway-analysis

  Public
  A webserver for pathway analysis of single cell trajectories

  Python

  •

  MIT License

  •0•0•1•0•Updated Jun 23, 2023Jun 23, 2023

• single-cell-pathway-analysis-client

  Public
  JavaScript

  •

  MIT License

  •0•0•0•0•Updated Jun 23, 2023Jun 23, 2023

• cptac-gbm-survival-signature

  Public
  In this analysis, we check if the survival transcriptomic signature in TCGA GBM cohort is also visible in the CPTAC GBM cohort.

  GNU Lesser General Public License v2.1

  •0•0•0•0•Updated Dec 30, 2022Dec 30, 2022

• causalpath-webserver

  Public
  Web Server for CausalPath

  CSS

  •

  GNU Lesser General Public License v3.0

  •2•4•4•10•Updated Dec 15, 2022Dec 15, 2022

• sif-explorer

  Public
  A web service for graph theoretic exploration of SIF networks.

  MIT License

  •0•0•0•0•Updated Oct 28, 2022Oct 28, 2022

• mutex

  Public
  Automatically exported from code.google.com/p/mutex

  Java

  •5•11•1•0•Updated Sep 22, 2022Sep 22, 2022

• Finkle-PHYS-479

  Public
  Python

  •

  GNU Lesser General Public License v2.1

  •1•0•4•0•Updated May 12, 2022May 12, 2022

• protein-site-motif

  Public
  This project aims to identify motifs in protein phosphorylation sites.

  Java

  •

  GNU Lesser General Public License v3.0

  •0•0•0•0•Updated Apr 25, 2022Apr 25, 2022

• misc-helpers

  Public
  Several miscellaneous python code for data processing and analysis.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 8, 2022Feb 8, 2022

• firehose-parser

  Public
  A parser for Broad Firehose

  Jupyter Notebook

  •

  GNU Lesser General Public License v2.1

  •0•0•0•0•Updated Nov 24, 2021Nov 24, 2021

• causality

  Public
  Automatically exported from code.google.com/p/causality

  Java

  •1•0•0•0•Updated Oct 12, 2021Oct 12, 2021

• misc

  Public
  Collection of several basic code

  Java

  •0•0•0•2•Updated Sep 10, 2021Sep 10, 2021

• cytoscape.js

  Public
  Graph theory (a.k.a. network) library for analysis and visualisation (compatible with CommonJS/Node.js/Browserify/Webpack, AMD/Require.js, npm, Bower, jspm, Meteor/Atmosphere, jQuery, and plain JS/JavaScript)

  JavaScript

  •

  MIT License

  •1.6k•0•0•0•Updated Jul 23, 2021Jul 23, 2021

• causal-priors-extractor

  Public
  This project extracts causal priors from Pathway Commons database to use in CausalPath.

  Java

  •

  GNU Lesser General Public License v2.1

  •0•0•0•0•Updated Feb 9, 2021Feb 9, 2021

• mutex-de-novo

  Public
  Mutual exclusivity analysis developed for de novo mutations in autism datasets.

  Java

  •

  GNU Lesser General Public License v3.0

  •1•1•0•1•Updated Oct 13, 2020Oct 13, 2020

• cancer-network

  Public
  For generating a network that shows the relations of the observed gene alterations in a cancer patient to the known cancer genes or other custom gene sets.

  Java

  •

  GNU Lesser General Public License v3.0

  •0•0•0•1•Updated Oct 12, 2020Oct 12, 2020

• modulators

  Public
  For discovering and classifying modulators of gene expression

  Java

  •

  GNU Lesser General Public License v3.0

  •0•0•0•0•Updated Sep 22, 2018Sep 22, 2018

• frext-to-biopax

  Public
  Convertor from REACH frext format to BioPAX

  Java

  •

  GNU Lesser General Public License v3.0

  •0•1•0•0•Updated Apr 9, 2018Apr 9, 2018

• tf-activity

  Public
  For inferring differential transcription factor activity using RNA expression data and transcriptional network.

  Java

  •

  GNU Lesser General Public License v3.0

  •0•1•0•0•Updated Oct 4, 2017Oct 4, 2017