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    52 repositories

    • DE-Bookdown

      Public
      Differential Expression Workshop
      HTML
      •
      Other
      •0•0•0•0•Updated Oct 27, 2025Oct 27, 2025

    • sarek

      Public
      Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
      Nextflow
      •
      MIT License
      •514•0•0•0•Updated Oct 16, 2025Oct 16, 2025

    • Metagenomics-Bookdown

      Public template
      TeX
      •
      Other
      •0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • ncgr-INBRE-Bookdown

      Public
      TeX
      •0•0•1•0•Updated Aug 1, 2025Aug 1, 2025

    • NIGMS-Sandbox-Pangenomics-Module

      Public
      HTML
      •
      Other
      •1•0•0•0•Updated May 2, 2025May 2, 2025

    • Adjudicator

      Public
      A tool for Adjudicating structural annotation evidence from genome assemblies
      Python
      •
      Apache License 2.0
      •0•0•3•0•Updated Apr 18, 2025Apr 18, 2025

    • Cyprinodon

      Public
      Pilot Project NNMC Cvar, Cbron, Cdes
      HTML
      •
      Other
      •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024

    • java

      Public
      Various Java apps written at NCGR for a variety of purposes.
      Java
      •3•5•0•0•Updated Aug 25, 2024Aug 25, 2024

    • NISE-bioinformatics

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Jul 24, 2024Jul 24, 2024

    • hyena-dna

      Public
      Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
      Assembly
      •
      Apache License 2.0
      •103•0•0•0•Updated Jun 15, 2024Jun 15, 2024

    • Coworking

      Public
      NCGR Coworking Studios
      HTML
      •0•0•0•0•Updated May 1, 2024May 1, 2024

    • NISE

      Public archive
      Summer Internship with NMSU
      HTML
      •
      Other
      •0•0•0•0•Updated Apr 16, 2024Apr 16, 2024

    • react-chatbots

      Public
      Chatbots built using React
      JavaScript
      •0•0•0•0•Updated Feb 22, 2024Feb 22, 2024

    • phapanmine

      Public
      Phaseolus pangenome mine (not an LIS mine)
      Java
      •
      GNU Lesser General Public License v3.0
      •2•0•0•0•Updated Dec 1, 2023Dec 1, 2023

    • CornBERT

      Public
      An implementatin of the CornBERT model
      Python
      •
      Apache License 2.0
      •0•0•3•0•Updated Aug 25, 2023Aug 25, 2023

    • SC_Best_Practices

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated May 22, 2023May 22, 2023

    • DE-workshop

      Public
      0•0•0•0•Updated Apr 13, 2023Apr 13, 2023

    • lis_sequence_search

      Public archive
      LIS sequence search
      JavaScript
      •0•2•3•9•Updated Jul 21, 2022Jul 21, 2022

    • aakbar

      Public archive
      Amino-Acid k-mer Tool
      Python
      •
      Other
      •3•0•0•16•Updated Jun 21, 2022Jun 21, 2022

    • seqtools2

      Public
      FASTX tools for manipulation, filtering, and sequence statistics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•1•1•Updated Jun 21, 2022Jun 21, 2022

    • alphabetsoup

      Public
      fix alphabet and gene length problems in protein FASTA files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•1•13•Updated Jul 29, 2021Jul 29, 2021

    • GFF3toolkit

      Public
      Python programs for processing GFF3 files
      Python
      •
      Other
      •27•0•0•0•Updated Jul 24, 2020Jul 24, 2020

    • biofletch

      Public
      Interchange of biological sequences and metadata between Apache Arrow and FASTA files
      Python
      •
      GNU General Public License v3.0
      •1•0•1•0•Updated Nov 19, 2019Nov 19, 2019

    • dotPlotly

      Public
      Generate an interactive dot plot from mummer or minimap alignments
      HTML
      •
      MIT License
      •60•1•0•0•Updated Oct 3, 2019Oct 3, 2019

    • MUTTools

      Public
      Tools for Visualizing and Manipulating Mutation Annotation Data
      Python
      •
      MIT License
      •0•0•0•0•Updated May 20, 2019May 20, 2019

    • cdbg

      Public
      A dynamic library and program for constructing and interacting with compressed de Bruijn graphs for pangenome analysis.
      C++
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 15, 2019May 15, 2019

    • BioMaptools

      Public
      Tools for Processing Biological Mapping Technologies
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 28, 2019Feb 28, 2019

    • BAli-Phy

      Public
      Bayesian co-estimation of phylogenies and multiple alignments via MCMC
      C++
      •
      GNU General Public License v2.0
      •18•0•0•0•Updated Dec 13, 2018Dec 13, 2018

    • UMI-analysis

      Public
      Scripts for processing Illumina sequence data containing unique molecular identifiers (UMI)
      C
      •
      Other
      •1•7•1•0•Updated Jul 6, 2018Jul 6, 2018

    • Dask_Interpro

      Public
      Dask Worker Processing of Interpro, with Resource Control
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 13, 2018Feb 13, 2018