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    172 repositories

    • voyager

      Public
      From geospatial to spatial -omics
      rexploratory-data-analysisspatial
      rexploratory-data-analysisspatialedarstatsbioconductorr-packageomicstranscriptomicsspatial-statistics
      R
      •
      Artistic License 2.0
      •14•103•22•0•Updated Apr 24, 2026Apr 24, 2026

    • SpatialFeatureExperiment

      Public
      Extension of SpatialExperiment with sf
      R
      •
      Artistic License 2.0
      •14•57•27•0•Updated Apr 24, 2026Apr 24, 2026

    • gget

      Public
      🧬 gget enables efficient querying of genomic reference databases
      rna-seqgenomicsreference
      rna-seqgenomicsreferencedatabasesensemblproteomicsblasttranscriptomicsuniprotncbi
      Python
      •
      BSD 2-Clause "Simplified" License
      •85•1.1k•22•1•Updated Apr 23, 2026Apr 23, 2026

    • monod

      Public
      The Monod package fits CME models to sequencing data.
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •7•33•3•0•Updated Apr 22, 2026Apr 22, 2026

    • tcia-radiology-processing

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Apr 20, 2026Apr 20, 2026

    • edgePython

      Public
      Repository for edgePython which is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count data.
      Python
      •
      GNU General Public License v3.0
      •6•68•0•0•Updated Apr 15, 2026Apr 15, 2026

    • OP_2025

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Apr 14, 2026Apr 14, 2026

    • LSCHWCP_202391

      Public
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Apr 13, 2026Apr 13, 2026

    • CJP_2025

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Apr 13, 2026Apr 13, 2026

    • rhopca

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•26•0•0•Updated Apr 13, 2026Apr 13, 2026

    • XgeneR

      Public
      HTML
      •
      BSD 2-Clause "Simplified" License
      •0•3•0•0•Updated Apr 8, 2026Apr 8, 2026

    • P_2026

      Public
      Repository for the paper "Spectral requirements for cooperation"
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Apr 6, 2026Apr 6, 2026

    • seqspec

      Public
      machine-readable file format for genomic library sequence and structure
      Python
      •
      MIT License
      •18•129•0•1•Updated Apr 3, 2026Apr 3, 2026

    • radiology_dataset_db

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Apr 2, 2026Apr 2, 2026

    • BI-BE-CS-183-2026

      Public
      Introduction to Computational Biology and Bioinformatics Course at Caltech, 2026
      Jupyter Notebook
      •
      Other
      •78•3•0•0•Updated Mar 31, 2026Mar 31, 2026

    • wompwomp

      Public
      R
      •
      Other
      •1•31•0•0•Updated Mar 30, 2026Mar 30, 2026

    • biowomp

      Public
      R
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Mar 30, 2026Mar 30, 2026

    • OP_2025_2

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Mar 20, 2026Mar 20, 2026

    • cellsweep

      Public
      Jupyter Notebook
      •0•22•0•0•Updated Mar 19, 2026Mar 19, 2026

    • kallisto

      Public
      Near-optimal RNA-Seq quantification
      rna-seqkallistopseudoalignment
      rna-seqkallistopseudoalignment
      C
      •
      BSD 2-Clause "Simplified" License
      •181•758•200•13•Updated Mar 16, 2026Mar 16, 2026

    • kb_docs

      Public
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Mar 12, 2026Mar 12, 2026

    • LSCHWCP_2023

      Public
      Identification of viral RdRPs in single-cell RNA sequencing data
      viruskallistotranslated
      viruskallistotranslatedviralpalmdbtranslated-alignmentcomma-free-code
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •2•13•1•0•Updated Mar 12, 2026Mar 12, 2026

    • kb_python

      Public
      A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
      scrna-seqkallistosingle-cell-rna-seq
      scrna-seqkallistosingle-cell-rna-seqrna-velocity-estimationbustoolskb-python
      Python
      •
      BSD 2-Clause "Simplified" License
      •29•186•0•0•Updated Mar 11, 2026Mar 11, 2026

    • kallistobustools

      Public
      kallisto | bustools workflow for pre-processing single-cell RNA-seq data
      rna-seqsingle-cellkallisto
      rna-seqsingle-cellkallistobustools
      MIT License
      •28•120•29•1•Updated Mar 10, 2026Mar 10, 2026

    • XgenePy

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Mar 5, 2026Mar 5, 2026

    • FCSKPP_2025

      Public
      R
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Feb 23, 2026Feb 23, 2026

    • gget_examples

      Public
      Examples for gget (https://github.com/pachterlab/gget).
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •6•39•0•0•Updated Feb 20, 2026Feb 20, 2026

    • 8cubeDB

      Public
      Query gene specificity in the founder mouse strains
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•2•0•0•Updated Feb 12, 2026Feb 12, 2026

    • GP_2023

      Public
      Switching processes
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

    • HCP_2024

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•2•0•0•Updated Jan 28, 2026Jan 28, 2026
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