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    125 repositories

    • alevin-fry

      Public
      🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
      rna-seqquantificationtranscriptomicssingle-cell10xsingle-cell-rna-seqrust
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •17•190•22•0•Updated Jul 30, 2025Jul 30, 2025

    • seqproc

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•4•1•Updated Jul 29, 2025Jul 29, 2025

    • piscem-infer

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •1•14•0•0•Updated Jul 20, 2025Jul 20, 2025

    • piscem

      Public
      Rust wrapper for the next generation (still currently in C++)
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•28•3•0•Updated Jul 15, 2025Jul 15, 2025

    • piscem-cpp

      Public
      A small sparse and fast reference index based on SSHash and Tiling encoding
      C
      •
      MIT License
      •1•6•0•0•Updated Jul 14, 2025Jul 14, 2025

    • lr_quant_benchmarks

      Public
      A replicable and modular benchmark for long-read RNA transcript quantification methods
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•6•1•1•Updated Jul 8, 2025Jul 8, 2025

    • QCatch

      Public
      Quality Control downstream of alevin-fry / simpleaf
      HTML
      •
      Other
      •0•3•0•0•Updated Jun 30, 2025Jun 30, 2025

    • oarfish

      Public
      long read RNA-seq quantification
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •5•89•2•1•Updated Jun 29, 2025Jun 29, 2025

    • minspace

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Jun 12, 2025Jun 12, 2025

    • cuttlefish

      Public
      Building the compacted de Bruijn graph efficiently from references or reads.
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •11•90•18•1•Updated May 1, 2025May 1, 2025

    • simpleaf

      Public
      A rust framework to make using alevin-fry even simpler
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •5•56•15•0•Updated Apr 29, 2025Apr 29, 2025

    • af-anndata

      Public
      alevin-fry related processing of AnnData
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•1•0•Updated Apr 29, 2025Apr 29, 2025

    • QCatch-resources

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 14, 2025Apr 14, 2025

    • alevin-fry-atac

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Apr 2, 2025Apr 2, 2025

    • pipfp-rs

      Public
      A Rust implementation of pipfp
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 1, 2025Apr 1, 2025

    • oarfish-paper-scripts

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 27, 2025Mar 27, 2025

    • seqcol_rs

      Public
      (unofficial) Rust implementation of SeqCol sequence collections
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 25, 2025Mar 25, 2025

    • rsrs

      Public
      Reference Signatures (rs) in Rust (rs)
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Mar 23, 2025Mar 23, 2025

    • isa-l

      Public
      Intelligent Storage Acceleration Library
      C
      •
      Other
      •327•0•0•0•Updated Mar 19, 2025Mar 19, 2025

    • combine-lab.github.io

      Public
      HTML
      •9•9•1•1•Updated Mar 7, 2025Mar 7, 2025

    • roers

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•0•0•Updated Jan 24, 2025Jan 24, 2025

    • grangers

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•17•0•0•Updated Jan 24, 2025Jan 24, 2025

    • efgdl-spec

      Public
      Specification for the extended fragment geometry description language
      BSD 3-Clause "New" or "Revised" License
      •0•4•0•0•Updated Jan 7, 2025Jan 7, 2025

    • pyroe

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•16•1•0•Updated Jan 6, 2025Jan 6, 2025

    • libradicl

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•0•0•Updated Dec 8, 2024Dec 8, 2024

    • lr-rna-sim-scripts

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • pufferfish

      Public
      An efficient index for the colored, compacted, de Bruijn graph
      indexdebruijndebruijn-graphgenomehashdbgcontigs
      C
      •
      GNU General Public License v3.0
      •22•111•24•3•Updated Oct 7, 2024Oct 7, 2024

    • kde-rs

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 31, 2024Aug 31, 2024

    • radtk

      Public
      Various tools for working with RAD files
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•1•0•Updated Aug 5, 2024Aug 5, 2024

    • kmers

      Public
      A bit-packed k-mer representation (and relevant utilities) for rust
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •9•48•7•1•Updated Jun 26, 2024Jun 26, 2024