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    32 repositories

    • gsplot

      Public
      Gene set viewer
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 8, 2026Feb 8, 2026

    • z-aggregate

      Public
      Jupyter Notebook
      •
      GNU Lesser General Public License v2.1
      •0•0•0•0•Updated Jan 29, 2026Jan 29, 2026

    • repo

      Public
      Repository for maven jars and other resources.
      0•0•0•0•Updated Dec 5, 2025Dec 5, 2025

    • 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

    • 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-biologyproteomicspathwaysphosphoproteomicscausality-analysispathway-analysis
      Java
      •
      GNU Lesser General Public License v3.0
      •11•45•7•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
      •22•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•1•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, Met…
      JavaScript
      •
      MIT License
      •1.7k•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