Repositories list

• deSRA

  Public
  An automated protocol to extract variation or expression from public NGS datasets

  JavaScript

  •

  MIT License

  •7•9•1•1•Updated Mar 28, 2024Mar 28, 2024

• LabPype

  Public
  Framework for Creating Pipeline Software

  frameworkvisualprogrammingworkflow+ 2widgetpipeline

  Python

  •

  Other

  •4•21•3•0•Updated Nov 15, 2023Nov 15, 2023

• Semantic-search-log-analysis-pipeline

  Public
  Classify web visitor queries so you can chart, and respond to, trends in information seeking

  searchmachine-learninglogs+ 3classificationnlm-oct2019umls

  JavaScript

  •

  MIT License

  •3•14•1•0•Updated Sep 7, 2023Sep 7, 2023

• MutPredMerge

  Public
  Consolidation of tools in the MutPred Suite to work with VCF files

  Python

  •

  MIT License

  •2•5•3•0•Updated Jul 19, 2023Jul 19, 2023

• deVoReaNN

  Public
  A virtual reality environment for physically assembling deep learning models to solve data science problems.

  C#

  •

  MIT License

  •2•12•0•4•Updated Jul 6, 2023Jul 6, 2023

• Phenogeno_Viz

  Public
  Ruby

  •

  MIT License

  •0•1•0•10•Updated Jan 19, 2023Jan 19, 2023

• The-Broad-Institute-Single-Cell-RNA-Seq-Data-Set

  Public
  Visualize cancer genomes with FAIR single-cell RNA-seq data

  cancer-genomicssingle-cell-genomicsfair-data+ 1chromosome-abberations

  Python

  •

  MIT License

  •6•11•5•18•Updated Jan 5, 2023Jan 5, 2023

• FAIRy-COMPASS

  Public
  FAIRness assessment for NCBI Hackathon products

  Python

  •

  MIT License

  •0•4•0•4•Updated Jan 3, 2023Jan 3, 2023

• iMETRIC

  Public
  Automated combinatorial epitope analysis from TCR clones

  Python

  •

  Apache License 2.0

  •1•2•0•11•Updated Dec 26, 2022Dec 26, 2022

• TriFECTA

  Public
  The goal of this project is use natural language processing to extract exclusion and inclusion criteria from free form text fields to match patients with clinical trials.

  Shell

  •

  MIT License

  •3•5•0•2•Updated Dec 8, 2022Dec 8, 2022

• PhenVar2

  Public
  A complete rewrite of the original PhenVar to enhance functionality and maintainability

  Python

  •

  MIT License

  •0•2•4•4•Updated Dec 8, 2022Dec 8, 2022

• SafeDrugs

  Public
  A web framework for interacting with drug safety data

  jupyterdashreactions+ 3drugnotebooksadverse

  Jupyter Notebook

  •

  MIT License

  •5•4•4•11•Updated Dec 8, 2022Dec 8, 2022

• RNA-Seq-in-the-Cloud

  Public
  An Easy to Use Analysis System for All Human Public bulk RNAseq Data!

  Jupyter Notebook

  •

  MIT License

  •21•18•9•25•Updated Dec 8, 2022Dec 8, 2022

• ClusterDuck

  Public
  Disease Clustering from Literature Based on Minimal Training Data

  snpsclusteringcorpus+ 3pubmedliteraturencbi

  Python

  •

  MIT License

  •6•7•6•23•Updated Nov 22, 2022Nov 22, 2022

• PubRunner

  Public
  Framework for running text mining tools on latest publications. Main page at:

  JavaScript

  •

  MIT License

  •7•14•1•0•Updated Jul 13, 2022Jul 13, 2022

• seqr

  Public
  Java

  •

  Creative Commons Zero v1.0 Universal

  •2•12•14•7•Updated May 20, 2022May 20, 2022

• Pipeline-for-Design-of-Patient-Specific-Disease-Progression-Phenotypes

  Public
  womenled-nih-2019

  R

  •

  MIT License

  •6•1•0•0•Updated Jan 29, 2022Jan 29, 2022

• SimpleGeneExpression

  Public
  Programs to quantify expression of transcripts from public datasets

  R

  •

  MIT License

  •2•9•1•0•Updated Nov 12, 2021Nov 12, 2021

• Enterococcus_Mobile_Elements

  Public template
  Identification of Mobile Elements in Enterococcae with a Focus on AMR Genes

  MIT License

  •5•2•0•0•Updated Oct 13, 2021Oct 13, 2021

• Nasty_Metagenomes

  Public
  Antimicrobial Resistance Characterization in Metagenomes

  Nextflow

  •

  MIT License

  •0•3•0•0•Updated Sep 1, 2021Sep 1, 2021

• Virulence_Factor_Characterization

  Public
  Virulence Factor Characterization in Metagenomes

  Jupyter Notebook

  •

  MIT License

  •5•7•0•0•Updated Aug 30, 2021Aug 30, 2021

• Viral-VDAP

  Public
  Viral VDAP: a viral alignment, variant discovery, and annotation pipeline launched at the NCBI-Hackathon 2019

  womenled-nih-2019

  Python

  •

  MIT License

  •6•5•0•0•Updated Aug 26, 2021Aug 26, 2021

• MetaClaMP-ML

  Public
  MetaClaMP-ML (Metagenome Classification of Metabolic Profiles using Machine Learning)

  microbial-virulence-hackathon

  Perl

  •

  MIT License

  •2•2•0•0•Updated Aug 23, 2021Aug 23, 2021

• Virulence_AMR_Data_Index_Resource

  Public
  Indexing and Visualization for AMRs and Virulence Genes in Genomes and Metagenomes

  HTML

  •

  MIT License

  •1•1•0•0•Updated Aug 20, 2021Aug 20, 2021

• Metatranscriptomics_Pilot

  Public
  A Pilot Project for Read Counts, Novel Transcripts and Population Level Functions in Metatranscriptomes

  microbial-virulence-hackathon

  Jupyter Notebook

  •

  MIT License

  •2•2•1•0•Updated Aug 20, 2021Aug 20, 2021

• NCBI_August_Hackathon_Push_Button_Genomics_Solution

  Public
  Python

  •

  Creative Commons Zero v1.0 Universal

  •2•5•10•3•Updated Jun 10, 2021Jun 10, 2021

• STREAMclean

  Public
  A simple command line tool to map SRA reads with high accuracy

  Python

  •

  MIT License

  •3•3•9•3•Updated Jun 1, 2021Jun 1, 2021

• seqr-tokenizer

  Public
  Java

  •1•2•0•3•Updated May 12, 2021May 12, 2021

• solr-tanimoto

  Public
  Java

  •1•4•0•3•Updated May 12, 2021May 12, 2021

• Salphagome

  Public
  Novel Discovery of Phages from Salmonella Sequences

  Jupyter Notebook

  •

  MIT License

  •2•2•10•0•Updated May 6, 2021May 6, 2021