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@acidgenomics Acid Genomics

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    38 repositories

    • koopa

      Public
      Shell bootloader for data science.
      Shell
      •
      GNU Affero General Public License v3.0
      •1•10•11•1•Updated Apr 29, 2026Apr 29, 2026

    • dotfiles

      Public
      Configuration files shared between machines.
      Vim Script
      •
      GNU Affero General Public License v3.0
      •0•1•1•0•Updated Apr 28, 2026Apr 28, 2026

    • py-acidbase

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•3•Updated Apr 14, 2026Apr 14, 2026

    • py-syntactic

      Public
      Make syntactically valid names out of strings.
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•3•Updated Apr 14, 2026Apr 14, 2026

    • py-goalie

      Public
      Assertive check functions for defensive Python programming.
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•1•3•Updated Apr 14, 2026Apr 14, 2026

    • py-acidplyr

      Public
      A pandas-based grammar for data frame manipulation.
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•3•Updated Apr 14, 2026Apr 14, 2026

    • py-acidgenomes

      Public
      Toolkit for downloading and processing genome annotations.
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•4•Updated Apr 14, 2026Apr 14, 2026

    • py-pipette

      Public
      Unified import and export of data in Python.
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•5•3•Updated Apr 14, 2026Apr 14, 2026

    • py-cellosaurus

      Public
      Cellosaurus identifier mapping toolkit.
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•3•Updated Apr 14, 2026Apr 14, 2026

    • r-aciddevtools

      Public
      Trusty sidekick for R package development.
      R
      •
      GNU Affero General Public License v3.0
      •0•3•0•0•Updated Mar 2, 2026Mar 2, 2026

    • 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 2, 2026Mar 2, 2026

    • r-cellosaurus

      Public
      Cellosaurus identifier mapping toolkit.
      R
      •
      GNU Affero General Public License v3.0
      •1•4•0•0•Updated Feb 25, 2026Feb 25, 2026

    • r-acidbase

      Public
      Base functions imported by Acid Genomics packages.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Feb 14, 2026Feb 14, 2026

    • 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-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-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•5•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-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
      •0•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•8•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
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