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    120 repositories

    • piscem-cpp

      Public
      A small sparse and fast reference index based on SShash and Tiling encoding
      C
      •
      MIT License
      •1•6•1•0•Updated Jan 21, 2025Jan 21, 2025

    • oarfish

      Public
      long read RNA-seq quantification
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •4•73•3•1•Updated Jan 20, 2025Jan 20, 2025

    • roers

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•0•1•Updated Jan 20, 2025Jan 20, 2025

    • grangers

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•17•0•1•Updated Jan 20, 2025Jan 20, 2025

    • af-anndata

      Public
      alevin-fry related processing of AnnData
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 18, 2025Jan 18, 2025

    • piscem

      Public
      Rust wrapper for the next generation (still currently in C++)
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •1•22•3•0•Updated Jan 13, 2025Jan 13, 2025

    • simpleaf

      Public
      A rust framework to make using alevin-fry even simpler
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •5•47•13•0•Updated Jan 10, 2025Jan 10, 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

    • seqproc

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•4•0•Updated Jan 7, 2025Jan 7, 2025

    • pyroe

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

    • 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
      •15•176•20•0•Updated Dec 24, 2024Dec 24, 2024

    • libradicl

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•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

    • alevin-fry-atac

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

    • cuttlefish

      Public
      Building the compacted de Bruijn graph efficiently from references or reads.
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •9•85•14•2•Updated Nov 14, 2024Nov 14, 2024

    • seqcol_rs

      Public
      (unofficial) Rust implementation of SeqCol sequence collections
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

    • cuttlefish-private

      Public
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • combine-lab.github.io

      Public
      HTML
      •7•8•0•1•Updated Oct 28, 2024Oct 28, 2024

    • pufferfish

      Public
      An efficient index for the colored, compacted, de Bruijn graph
      indexdebruijndebruijn-graphgenomehashdbgcontigs
      C
      •
      GNU General Public License v3.0
      •20•108•23•2•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

    • 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•5•1•1•Updated Aug 16, 2024Aug 16, 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
      •10•47•7•1•Updated Jun 26, 2024Jun 26, 2024

    • RapClust

      Public
      Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes
      Python
      •
      Other
      •6•30•6•1•Updated Jun 16, 2024Jun 16, 2024

    • salmon

      Public
      🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
      bioinformaticsrna-seqgene-expressionrnaseqscrna-seqquantificationsingle-cellsailfish10xsingle-cell-rna-seq
      C++
      •
      GNU General Public License v3.0
      •164•784•363•3•Updated May 29, 2024May 29, 2024

    • TreeTerminus

      Public
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•1•0•Updated Apr 17, 2024Apr 17, 2024

    • forseti-experiments

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 4, 2024Apr 4, 2024

    • rsrs

      Public
      Reference Signatures (rs) in Rust (rs)
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Apr 1, 2024Apr 1, 2024

    • quantaf

      Public
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •2•8•0•1•Updated Mar 2, 2024Mar 2, 2024

    • simplr

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Feb 28, 2024Feb 28, 2024