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    35 repositories

    • skimgpt

      Public
      Evaluate hypotheses at scale.
      Python
      •1•4•5•0•Updated Oct 20, 2025Oct 20, 2025

    • fast_km

      Public
      A Containerized KinderMiner / Serial KinderMiner Server
      text-miningbioinformatics
      Python
      •
      MIT License
      •2•0•0•2•Updated Oct 13, 2025Oct 13, 2025

    • scRNAseq_downstream

      Public
      Code for the analysis of the pig retinal organoid data from David Gamm
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Aug 26, 2025Aug 26, 2025

    • scRNAseq_library

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • seqtools

      Public
      dockerized tools for tasks related to RNA-Seq
      R
      •
      MIT License
      •1•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • CutTag_library

      Public
      Code for processing cut and tag data
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 2, 2025Jan 2, 2025

    • LiFang_scRNAseq

      Public
      single cell RNA seq scripts for Li Fang Jack's fluidigm data
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • rms_pkgs

      Public
      Jupyter Notebook
      •
      Other
      •0•1•3•0•Updated Nov 20, 2024Nov 20, 2024

    • cmdlogtime

      Public
      Packaging of wrapper with logging, timing, and parameter histories
      Python
      •
      MIT License
      •33•0•0•0•Updated Jan 16, 2024Jan 16, 2024

    • GOSeqPy

      Public
      A Python wrapper around GOSeq
      Python
      •1•0•0•0•Updated Dec 19, 2023Dec 19, 2023

    • kinderminer_kg

      Public
      Build a knowledge graph from PubMed abstracts using KinderMiner, Prodigy, and spaCy
      Python
      •
      MIT License
      •0•6•0•0•Updated Jul 28, 2023Jul 28, 2023

    • GSVApy

      Public
      A Python wrapper around the GSVA algorithm
      Python
      •2•0•0•0•Updated Jun 27, 2023Jun 27, 2023

    • Johansson_2023_CRTAC1_manuscript_Rmd

      Public
      Statistical analysis of CRTAC1 concentrations in various patient groups
      HTML
      •0•0•0•0•Updated 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
      •805•0•0•0•Updated Mar 22, 2023Mar 22, 2023

    • calculator_yb

      Public
      MIT License
      •0•0•0•0•Updated Mar 6, 2023Mar 6, 2023

    • pr_demo

      Public
      Python
      •
      MIT License
      •0•1•0•1•Updated Jan 19, 2023Jan 19, 2023

    • Nile-rat-genome-curation-and-improvement

      Public
      0•0•2•0•Updated Dec 30, 2022Dec 30, 2022

    • GO_GENE_POST_PROCESSOR

      Public
      Python
      •0•0•0•0•Updated Dec 28, 2022Dec 28, 2022

    • VS-Code-Guide

      Public
      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. 
      0•0•1•0•Updated Nov 10, 2022Nov 10, 2022

    • calculator_rs

      Public
      Python
      •
      MIT License
      •2•1•0•0•Updated Nov 8, 2022Nov 8, 2022

    • JackCalc

      Public
      MIT License
      •1•0•0•1•Updated Oct 27, 2022Oct 27, 2022

    • blue_whale

      Public
      Blue whale project related scripts and small datasets
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jul 9, 2022Jul 9, 2022

    • ROC_and_PR

      Public
      Python
      •0•1•0•0•Updated Jul 6, 2022Jul 6, 2022

    • Heliobacter

      Public
      Jupyter Notebook
      •0•0•0•0•Updated 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
      •1•8•0•0•Updated Mar 29, 2021Mar 29, 2021

    • CHARTS

      Public
      CHARTS: Characterizing Tumor Subpopulations
      Python
      •
      MIT License
      •0•3•1•0•Updated Feb 10, 2021Feb 10, 2021

    • Figures-and-Supplementary-Figures---SKiM-Manuscript

      Public
      R
      •0•0•0•0•Updated Nov 3, 2020Nov 3, 2020

    • KinderMiner_2

      Public
      Python
      •0•0•0•0•Updated Sep 28, 2020Sep 28, 2020

    • Phenotypes_and_symptoms_lexicon

      Public
      Java
      •0•0•0•0•Updated Aug 28, 2020Aug 28, 2020

    • Expert_curated_disease_drug_associations

      Public
      Java
      •0•0•0•0•Updated Aug 28, 2020Aug 28, 2020