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    148 repositories

    • SpatialFeatureExperiment

      Public
      Extension of SpatialExperiment with sf
      R
      •
      Artistic License 2.0
      •13•55•28•2•Updated Aug 18, 2025Aug 18, 2025

    • varseek

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•6•0•0•Updated Aug 18, 2025Aug 18, 2025

    • voyager

      Public
      From geospatial to spatial -omics
      exploratory-data-analysisspatialedabioconductorr-packageomicstranscriptomicsspatial-statisticsesdaspatial-transcriptomics
      R
      •
      Artistic License 2.0
      •13•95•21•0•Updated Aug 15, 2025Aug 15, 2025

    • gget

      Public
      🧬 gget enables efficient querying of genomic reference databases
      rna-seqgenomicsreferencedatabasesensemblproteomicsblasttranscriptomicsuniprotncbi
      Python
      •
      BSD 2-Clause "Simplified" License
      •75•1k•19•1•Updated Aug 15, 2025Aug 15, 2025

    • seqspec

      Public
      machine-readable file format for genomic library sequence and structure
      Python
      •
      MIT License
      •17•121•3•0•Updated Aug 14, 2025Aug 14, 2025

    • varseek-examples

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

    • RLSRP_2025

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•2•0•0•Updated Aug 12, 2025Aug 12, 2025

    • OP_2025

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Aug 8, 2025Aug 8, 2025

    • pachterlab.github.io

      Public
      HTML
      •0•0•0•0•Updated Aug 6, 2025Aug 6, 2025

    • JBMMCKP_2023

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•5•0•0•Updated Aug 1, 2025Aug 1, 2025

    • LSCHWCP_2023

      Public
      Identification of viral RdRPs in single-cell RNA sequencing data
      viruskallistotranslatedviralpalmdbtranslated-alignmentcomma-free-code
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•11•1•0•Updated Jul 23, 2025Jul 23, 2025

    • kb_docs

      Public
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Jul 18, 2025Jul 18, 2025

    • LP_2021

      Public
      TeX
      •
      BSD 2-Clause "Simplified" License
      •6•49•1•0•Updated Jun 15, 2025Jun 15, 2025

    • splitcode

      Public
      Flexible and efficient parsing, interpreting and editing of sequencing reads
      C
      •
      BSD 2-Clause "Simplified" License
      •1•43•12•0•Updated Jun 15, 2025Jun 15, 2025

    • Chronocell

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•2•0•0•Updated Jun 13, 2025Jun 13, 2025

    • concordexR

      Public
      Compute the neighborhood consolidation matrix and identify SHRs
      R
      •
      Artistic License 2.0
      •0•13•1•0•Updated Jun 12, 2025Jun 12, 2025

    • XgeneR

      Public
      HTML
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Jun 12, 2025Jun 12, 2025

    • FGP_2024

      Public
      Jupyter Notebook
      •1•14•3•0•Updated Jun 10, 2025Jun 10, 2025

    • data

      Public
      Pachter lab datasets
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Jun 3, 2025Jun 3, 2025

    • sleuth

      Public
      Differential analysis of RNA-Seq
      rna-seq
      R
      •
      GNU General Public License v3.0
      •96•305•102•7•Updated May 28, 2025May 28, 2025

    • kb_python

      Public
      A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
      scrna-seqsingle-cell-rna-seqrna-velocity-estimationkallistobustoolskb-python
      Python
      •
      BSD 2-Clause "Simplified" License
      •25•166•2•1•Updated May 27, 2025May 27, 2025

    • GBP_2024

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•5•0•0•Updated May 26, 2025May 26, 2025

    • qcbc

      Public
      Jupyter Notebook
      •
      MIT License
      •4•20•0•0•Updated May 24, 2025May 24, 2025

    • CGCCP_2023

      Public
      scVI extension for unspliced RNA
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•16•1•0•Updated May 18, 2025May 18, 2025

    • gget_examples

      Public
      Examples for gget (https://github.com/pachterlab/gget).
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •6•38•0•0•Updated May 14, 2025May 14, 2025

    • SBP_2025

      Public
      Code for reproducing the results in the klue manuscript
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•2•0•0•Updated May 14, 2025May 14, 2025

    • klue

      Public
      HTML
      •
      BSD 2-Clause "Simplified" License
      •0•4•0•0•Updated May 14, 2025May 14, 2025

    • KP_2025

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•3•0•0•Updated May 13, 2025May 13, 2025

    • FP_2025

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•2•1•0•Updated May 12, 2025May 12, 2025

    • LSRRSRLFKOTWMWMP_2024

      Public
      Repository for reproducing results for lr-kallisto
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•9•0•0•Updated Apr 23, 2025Apr 23, 2025