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    135 repositories

    • SpatialFeatureExperiment

      Public
      Extension of SpatialExperiment with sf
      R
      •
      Artistic License 2.0
      •7•43•23•0•Updated Nov 20, 2024Nov 20, 2024

    • voyager

      Public
      From geospatial to spatial -omics
      exploratory-data-analysisspatialedabioconductorr-packageomicstranscriptomicsspatial-statisticsesdaspatial-transcriptomics
      R
      •
      Artistic License 2.0
      •9•79•12•0•Updated Nov 19, 2024Nov 19, 2024

    • kb_docs

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Nov 18, 2024Nov 18, 2024

    • alabaster.sfe

      Public
      Language agnostic on disk representation of SFE objects
      R
      •
      Other
      •1•0•0•0•Updated Nov 18, 2024Nov 18, 2024

    • gget

      Public
      🧬 gget enables efficient querying of genomic reference databases
      referencedatabasesensemblblastuniprotncbienrichment-analysisenrichralphafoldgget
      Python
      •
      BSD 2-Clause "Simplified" License
      •74•948•18•2•Updated Nov 15, 2024Nov 15, 2024

    • kallisto

      Public
      Near-optimal RNA-Seq quantification
      rna-seqkallistopseudoalignment
      C
      •
      BSD 2-Clause "Simplified" License
      •172•656•172•10•Updated Nov 14, 2024Nov 14, 2024

    • LSCHWCP_2023

      Public
      Identification of viral RNA in single-cell RNA sequencing data
      viruskallistotranslatedviralpalmdbtranslated-alignmentcomma-free-code
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•2•2•0•Updated Nov 13, 2024Nov 13, 2024

    • concordexR

      Public
      Compute the neighborhood consolidation matrix and identify SHRs
      R
      •
      Artistic License 2.0
      •0•13•1•0•Updated Nov 11, 2024Nov 11, 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

    • seqspec

      Public
      machine-readable file format for genomic library sequence and structure
      Python
      •
      MIT License
      •17•114•2•0•Updated Nov 4, 2024Nov 4, 2024

    • FGP_2024

      Public
      Jupyter Notebook
      •0•4•2•0•Updated Oct 30, 2024Oct 30, 2024

    • CGCCP_2023

      Public
      scVI extension for unspliced RNA
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•16•0•0•Updated Oct 28, 2024Oct 28, 2024

    • monod

      Public
      The Monod package fits CME models to sequencing data.
      Python
      •
      BSD 2-Clause "Simplified" License
      •3•30•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•154•2•1•Updated Oct 21, 2024Oct 21, 2024

    • CP_2023

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •5•7•1•0•Updated Oct 14, 2024Oct 14, 2024

    • GBP_2024

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•5•0•0•Updated Oct 6, 2024Oct 6, 2024

    • splitcode

      Public
      Flexible and efficient parsing, interpreting and editing of sequencing reads
      C
      •
      BSD 2-Clause "Simplified" License
      •2•41•13•1•Updated Oct 3, 2024Oct 3, 2024

    • snATAK

      Public
      BSD 2-Clause "Simplified" License
      •0•2•0•0•Updated Oct 2, 2024Oct 2, 2024

    • concordex

      Public
      Identification of spatial homogeneous regions
      Python
      •
      MIT License
      •1•19•1•0•Updated Oct 1, 2024Oct 1, 2024

    • qcbc

      Public
      Jupyter Notebook
      •
      MIT License
      •3•19•0•0•Updated Sep 16, 2024Sep 16, 2024

    • HSSHMP_2024

      Public
      0•1•0•0•Updated Sep 13, 2024Sep 13, 2024

    • LSRRSRLFKOTWMWMP_2024

      Public
      Repository for reproducing results for lr-kallisto
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•4•0•0•Updated Sep 12, 2024Sep 12, 2024

    • LP_2024

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•5•0•0•Updated Sep 5, 2024Sep 5, 2024

    • pachterlab.github.io

      Public
      HTML
      •0•0•0•0•Updated Sep 3, 2024Sep 3, 2024

    • Chronocell

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Aug 26, 2024Aug 26, 2024

    • ffq

      Public
      A tool to find sequencing data and metadata from public databases.
      Python
      •
      MIT License
      •47•551•0•3•Updated Aug 13, 2024Aug 13, 2024

    • CGP_2023

      Public
      Repository for meK-Means Inference Method
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•7•0•0•Updated Aug 7, 2024Aug 7, 2024

    • FGP_2023

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Jul 31, 2024Jul 31, 2024