Repositories list

• NIGMS-Sandbox-Pangenomics-Module

  Public
  HTML

  •

  MIT License

  •0•0•15•0•Updated Dec 20, 2024Dec 20, 2024

• ncgr-INBRE-Bookdown

  Public
  TeX

  •0•0•1•0•Updated Dec 19, 2024Dec 19, 2024

• Cyprinodon

  Public
  Pilot Project NNMC Cvar, Cbron, Cdes

  HTML

  •

  Other

  •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• DE-Bookdown

  Public
  Differential Expression Workshop

  HTML

  •

  Other

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• Metagenomics-Bookdown

  Public template
  TeX

  •

  Other

  •0•0•0•0•Updated Nov 8, 2024Nov 8, 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

  •85•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

  •55•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•1•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

  •17•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

• lis_gene_families

  Public
  HTML

  •1•0•0•0•Updated Nov 21, 2017Nov 21, 2017

• Polymer_Components

  Public
  A Test Repository for Web Component Standards

  HTML

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 26, 2017Oct 26, 2017