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    257 repositories

    • 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
      workflowframeworkwidget
      workflowframeworkwidgetpipelinevisualprogramming
      Python
      •
      Other
      •3•22•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
      searchmachine-learninglogsclassificationumlsnlm-oct2019
      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•6•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•13•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
      cancer-genomicssingle-cell-genomicsfair-datachromosome-abberationsbioit2019
      Python
      •
      MIT License
      •6•13•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 clinic…
      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
      jupyterdashreactionsdrugnotebooksadverse
      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•19•9•25•Updated Dec 8, 2022Dec 8, 2022

    • ClusterDuck

      Public
      Disease Clustering from Literature Based on Minimal Training Data
      snpsclusteringcorpus
      snpsclusteringcorpuspubmedliteraturencbi
      Python
      •
      MIT License
      •6•8•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
      •8•15•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
      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•3•0•0•Updated Oct 13, 2021Oct 13, 2021

    • Nasty_Metagenomes

      Public
      Antimicrobial Resistance Characterization in Metagenomes
      Nextflow
      •
      MIT License
      •0•4•0•0•Updated Sep 1, 2021Sep 1, 2021

    • Virulence_Factor_Characterization

      Public
      Virulence Factor Characterization in Metagenomes
      Jupyter Notebook
      •
      MIT License
      •5•9•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
      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
      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
      microbial-virulence-hackathon
      Jupyter Notebook
      •
      MIT License
      •1•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
      •4•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•5•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
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