Repositories list

• 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 Oct 29, 2024Oct 29, 2024

• scRNAseq_library

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

• fast_km

  Public
  A Containerized KinderMiner / Serial KinderMiner Server

  text-miningbioinformatics

  Python

  •

  MIT License

  •2•0•0•0•Updated Aug 15, 2024Aug 15, 2024

• LiFang_scRNAseq

  Public
  single cell RNA seq scripts for Li Fang Jack's fluidigm data

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Apr 18, 2024Apr 18, 2024

• cmdlogtime

  Public
  Packaging of wrapper with logging, timing, and parameter histories

  Python

  •

  MIT License

  •34•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•5•0•0•Updated Jul 28, 2023Jul 28, 2023

• rms_pkgs

  Public
  Jupyter Notebook

  •

  Other

  •0•1•3•0•Updated Jun 27, 2023Jun 27, 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

  •705•0•0•0•Updated Mar 22, 2023Mar 22, 2023

• calculator_yb

  Public
  MIT License

  •1•0•0•1•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

• Drugs_subset_for_drugs_repurposing_application

  Public
  Java

  •0•0•0•0•Updated Aug 27, 2020Aug 27, 2020

• Diseases_lexicon

  Public
  Diseases Lexicon

  Java

  •0•0•0•0•Updated Aug 27, 2020Aug 27, 2020

• kinderminer_webapp

  Public
  Code for the KinderMiner web application

  Python

  •

  MIT License

  •1•0•0•0•Updated Jul 15, 2020Jul 15, 2020