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@acidgenomics Acid Genomics

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    31 repositories

    • koopa

      Public
      Shell bootloader for bioinformatics.
      Shell
      •
      GNU Affero General Public License v3.0
      •1•11•6•0•Updated Aug 8, 2025Aug 8, 2025

    • dotfiles

      Public
      Configuration files shared between machines.
      Vim Script
      •
      GNU Affero General Public License v3.0
      •0•0•1•0•Updated Aug 6, 2025Aug 6, 2025

    • r-panther

      Public
      PANTHER database annotations.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated May 26, 2025May 26, 2025

    • r-eggnog

      Public
      EggNOG database annotations.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated May 26, 2025May 26, 2025

    • r-acidtest

      Public
      Reference data for Acid Genomics unit tests.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated May 25, 2025May 25, 2025

    • r-aciddevtools

      Public
      Trusty sidekick for R package development.
      R
      •
      GNU Affero General Public License v3.0
      •0•3•0•0•Updated May 25, 2025May 25, 2025

    • r-acidcli

      Public
      Interative R command line interface toolkit.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Apr 25, 2025Apr 25, 2025

    • r-acidbase

      Public
      Low-level base functions imported by Acid Genomics packages.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Apr 24, 2025Apr 24, 2025

    • r-acidgenerics

      Public
      S4 generic functions for Acid Genomics packages.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Apr 24, 2025Apr 24, 2025

    • r-acidgenomes

      Public
      Toolkit for downloading and processing genome annotations.
      R
      •
      GNU Affero General Public License v3.0
      •0•4•2•0•Updated Apr 22, 2025Apr 22, 2025

    • r-acidsinglecell

      Public
      Toolkit for single-cell RNA-seq analysis that extends the functionality of SingleCellExperiment.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Apr 12, 2025Apr 12, 2025

    • r-acidexperiment

      Public
      Toolkit to extend the functionality of SummarizedExperiment.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Apr 12, 2025Apr 12, 2025

    • r-cellosaurus

      Public
      Cellosaurus identifier mapping toolkit.
      R
      •
      GNU Affero General Public License v3.0
      •1•3•0•0•Updated Mar 24, 2025Mar 24, 2025

    • r-acidgsea

      Public
      Parameterized fast gene set enrichment analysis.
      R
      •
      GNU Affero General Public License v3.0
      •0•2•0•0•Updated Mar 24, 2025Mar 24, 2025

    • r-deseqanalysis

      Public
      Toolkit for performing differential expression with DESeq2.
      R
      •
      GNU Affero General Public License v3.0
      •1•3•0•0•Updated Mar 24, 2025Mar 24, 2025

    • r-basejump

      Public
      Base functions for bioinformatics and R package development.
      R
      •
      GNU Affero General Public License v3.0
      •3•5•0•0•Updated Mar 24, 2025Mar 24, 2025

    • r-acidplots

      Public
      Functions for plotting genomic data.
      R
      •
      GNU Affero General Public License v3.0
      •1•5•0•0•Updated Mar 24, 2025Mar 24, 2025

    • r-acidroxygen

      Public
      Shared roxygen2 documentation for Acid Genomics packages.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Mar 24, 2025Mar 24, 2025

    • r-acidmarkdown

      Public
      Toolkit for extending the functionality of R Markdown.
      TeX
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Mar 24, 2025Mar 24, 2025

    • r-acidplyr

      Public
      A grammar of S4 class data manipulation.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Mar 24, 2025Mar 24, 2025

    • r-pipette

      Public
      Pipette biological data in and out of R.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•1•0•Updated Mar 24, 2025Mar 24, 2025

    • r-syntactic

      Public
      Make syntactically valid names out of character vectors.
      R
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated Mar 24, 2025Mar 24, 2025

    • r-goalie

      Public
      Assertive check functions for defensive R programming.
      R
      •
      GNU Affero General Public License v3.0
      •0•3•0•0•Updated Mar 21, 2025Mar 21, 2025

    • r-bcbiosinglecell

      Public archive
      R package for bcbio single-cell RNA-seq analysis.
      R
      •
      GNU Affero General Public License v3.0
      •8•0•0•0•Updated Sep 9, 2024Sep 9, 2024

    • r-bcbiornaseq

      Public archive
      R package for bcbio RNA-seq analysis.
      R
      •
      GNU Affero General Public License v3.0
      •21•0•0•0•Updated Sep 9, 2024Sep 9, 2024

    • r-bcbiobase

      Public archive
      Base functions for bcbio R packages.
      R
      •
      GNU Affero General Public License v3.0
      •3•0•0•0•Updated Sep 9, 2024Sep 9, 2024

    • docker

      Public
      Dockerfile recipes for the Acid Genomics Docker Hub images.
      Dockerfile
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jul 15, 2024Jul 15, 2024

    • r-pointillism

      Public
      R package for for single-cell RNA-seq clustering analysis.
      R
      •
      GNU Affero General Public License v3.0
      •2•5•0•0•Updated Apr 4, 2024Apr 4, 2024

    • r-chromium

      Public
      Toolkit for 10X Genomics Chromium single cell data.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Dec 5, 2023Dec 5, 2023

    • latch-sdk

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Oct 25, 2023Oct 25, 2023