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    138 repositories

    • SpatialFeatureExperiment

      Public
      Extension of SpatialExperiment with sf
      R
      •
      Artistic License 2.0
      •10•47•22•0•Updated Feb 11, 2025Feb 11, 2025

    • KP_2025

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Feb 10, 2025Feb 10, 2025

    • fastQpick

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•22•0•0•Updated Feb 10, 2025Feb 10, 2025

    • gget

      Public
      🧬 gget enables efficient querying of genomic reference databases
      referencedatabasesensemblblastuniprotncbienrichment-analysisenrichralphafoldgget
      Python
      •
      BSD 2-Clause "Simplified" License
      •76•985•17•2•Updated Feb 8, 2025Feb 8, 2025

    • RMEJLBASBMP_2024

      Public
      Repository for the paper "The impact of package selection and versioning on single-cell RNA-seq analysis"
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •5•18•0•0•Updated Feb 7, 2025Feb 7, 2025

    • kb_docs

      Public
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Feb 7, 2025Feb 7, 2025

    • pachterlab.github.io

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

    • alabaster.sfe

      Public
      Language agnostic on disk representation of SFE objects
      R
      •
      Other
      •2•0•2•0•Updated Feb 6, 2025Feb 6, 2025

    • FGP_2024

      Public
      Jupyter Notebook
      •1•10•3•0•Updated Feb 6, 2025Feb 6, 2025

    • BI-1C-2024

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•1•0•0•Updated Feb 4, 2025Feb 4, 2025

    • voyager

      Public
      From geospatial to spatial -omics
      exploratory-data-analysisspatialedabioconductorr-packageomicstranscriptomicsspatial-statisticsesdaspatial-transcriptomics
      R
      •
      Artistic License 2.0
      •10•85•16•0•Updated Jan 30, 2025Jan 30, 2025

    • gget_examples

      Public
      Examples for gget (https://github.com/pachterlab/gget).
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •5•30•0•0•Updated Jan 23, 2025Jan 23, 2025

    • seqspec

      Public
      machine-readable file format for genomic library sequence and structure
      Python
      •
      MIT License
      •17•118•5•2•Updated Jan 22, 2025Jan 22, 2025

    • CGCCP_2023

      Public
      scVI extension for unspliced RNA
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•16•1•0•Updated Jan 20, 2025Jan 20, 2025

    • concordexR

      Public
      Compute the neighborhood consolidation matrix and identify SHRs
      R
      •
      Artistic License 2.0
      •0•13•1•0•Updated Jan 17, 2025Jan 17, 2025

    • JBMMCKP_2023

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•5•0•0•Updated Jan 16, 2025Jan 16, 2025

    • concordex

      Public
      Identification of spatial homogeneous regions
      Python
      •
      MIT License
      •1•19•1•0•Updated Jan 14, 2025Jan 14, 2025

    • splitcode-tutorial

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Jan 8, 2025Jan 8, 2025

    • splitcode

      Public
      Flexible and efficient parsing, interpreting and editing of sequencing reads
      C
      •
      BSD 2-Clause "Simplified" License
      •2•41•11•0•Updated Jan 7, 2025Jan 7, 2025

    • FLP_2024

      Public
      Repository for the virial theorem and Price equation paper
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Dec 31, 2024Dec 31, 2024

    • 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•4•2•0•Updated Dec 28, 2024Dec 28, 2024

    • LSRRSRLFKOTWMWMP_2024

      Public
      Repository for reproducing results for lr-kallisto
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•5•0•0•Updated Dec 18, 2024Dec 18, 2024

    • SFEData

      Public
      Example SpatialFeatureExperiment datasets
      R
      •
      Artistic License 2.0
      •0•2•1•0•Updated Dec 18, 2024Dec 18, 2024

    • qcbc

      Public
      Jupyter Notebook
      •
      MIT License
      •4•19•0•1•Updated Dec 9, 2024Dec 9, 2024

    • kallisto

      Public
      Near-optimal RNA-Seq quantification
      rna-seqkallistopseudoalignment
      C
      •
      BSD 2-Clause "Simplified" License
      •173•673•181•10•Updated Dec 3, 2024Dec 3, 2024

    • monod_examples

      Public
      Tutorials for the Monod package, which fits CME models to sequencing data.
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•6•2•0•Updated Nov 6, 2024Nov 6, 2024

    • BI-1C-2025

      Public
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Nov 5, 2024Nov 5, 2024

    • monod

      Public
      The Monod package fits CME models to sequencing data.
      Python
      •
      BSD 2-Clause "Simplified" License
      •3•31•3•0•Updated Oct 26, 2024Oct 26, 2024

    • SHSOHMP_2024

      Public
      Code for reproducing the results in the second version of the preprint "Accurate quantification of single-nucleus and single-cell RNA-seq transcripts"
      C++
      •
      BSD 2-Clause "Simplified" License
      •1•5•0•0•Updated Oct 25, 2024Oct 25, 2024

    • 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
      •23•159•3•1•Updated Oct 21, 2024Oct 21, 2024