Skip to content
Change the repository type filter

All

    Repositories list

    • Code for the analysis of the pig retinal organoid data from David Gamm
      Jupyter Notebook
      MIT License
      0200Updated Oct 29, 2024Oct 29, 2024
    • Jupyter Notebook
      MIT License
      0000Updated Sep 30, 2024Sep 30, 2024
    • fast_km

      Public
      A Containerized KinderMiner / Serial KinderMiner Server
      Python
      MIT License
      2000Updated Aug 15, 2024Aug 15, 2024
    • single cell RNA seq scripts for Li Fang Jack's fluidigm data
      Jupyter Notebook
      MIT License
      0000Updated Apr 18, 2024Apr 18, 2024
    • Packaging of wrapper with logging, timing, and parameter histories
      Python
      MIT License
      34000Updated Jan 16, 2024Jan 16, 2024
    • GOSeqPy

      Public
      A Python wrapper around GOSeq
      Python
      1000Updated Dec 19, 2023Dec 19, 2023
    • Build a knowledge graph from PubMed abstracts using KinderMiner, Prodigy, and spaCy
      Python
      MIT License
      0500Updated Jul 28, 2023Jul 28, 2023
    • rms_pkgs

      Public
      Jupyter Notebook
      Other
      0130Updated Jun 27, 2023Jun 27, 2023
    • GSVApy

      Public
      A Python wrapper around the GSVA algorithm
      Python
      2000Updated Jun 27, 2023Jun 27, 2023
    • Statistical analysis of CRTAC1 concentrations in various patient groups
      HTML
      0000Updated Apr 11, 2023Apr 11, 2023
    • rnaseq

      Public
      RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
      Nextflow
      MIT License
      705000Updated Mar 22, 2023Mar 22, 2023
    • MIT License
      1001Updated Mar 6, 2023Mar 6, 2023
    • pr_demo

      Public
      Python
      MIT License
      0101Updated Jan 19, 2023Jan 19, 2023
    • 0020Updated Dec 30, 2022Dec 30, 2022
    • Python
      0000Updated Dec 28, 2022Dec 28, 2022
    • This guide serves as a starting point to configure VSCode to work with our servers. By the end of this guide, one should be ready to create, edit, and manage files on our servers while taking advantage of Git for version control. This tutorial assumes you have no necessary extensions, dependencies or applications pre-installed. 
      0010Updated Nov 10, 2022Nov 10, 2022
    • Python
      MIT License
      2100Updated Nov 8, 2022Nov 8, 2022
    • JackCalc

      Public
      MIT License
      1001Updated Oct 27, 2022Oct 27, 2022
    • Blue whale project related scripts and small datasets
      R
      GNU General Public License v3.0
      0100Updated Jul 9, 2022Jul 9, 2022
    • Python
      0100Updated Jul 6, 2022Jul 6, 2022
    • Jupyter Notebook
      0000Updated May 31, 2022May 31, 2022
    • SKiM

      Public
      Serial KinderMiner (or simply SKiM) is general literature-based discovery system for querying all ~30 million PubMed abstracts.
      Python
      1800Updated Mar 29, 2021Mar 29, 2021
    • CHARTS

      Public
      CHARTS: Characterizing Tumor Subpopulations
      Python
      MIT License
      0310Updated Feb 10, 2021Feb 10, 2021
    • R
      0000Updated Nov 3, 2020Nov 3, 2020
    • Python
      0000Updated Sep 28, 2020Sep 28, 2020
    • Java
      0000Updated Aug 28, 2020Aug 28, 2020
    • Java
      0000Updated Aug 28, 2020Aug 28, 2020
    • Java
      0000Updated Aug 27, 2020Aug 27, 2020
    • Diseases Lexicon
      Java
      0000Updated Aug 27, 2020Aug 27, 2020
    • Code for the KinderMiner web application
      Python
      MIT License
      1000Updated Jul 15, 2020Jul 15, 2020