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    71 repositories

    • orbit

      Public
      Rust wrapper for STAR aligner
      C
      •
      MIT License
      •3•17•0•4•Updated Mar 27, 2025Mar 27, 2025

    • analysis_guides

      Public
      10x Genomics analysis guides files
      Jupyter Notebook
      •10•8•1•0•Updated Mar 27, 2025Mar 27, 2025

    • bamtofastq

      Public
      Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
      Rust
      •
      MIT License
      •7•62•17•13•Updated Mar 25, 2025Mar 25, 2025

    • rules_conda

      Public
      Bazel rules for creating conda environments
      condabazel-rulesconda-environmentbazel-deps
      Go
      •
      MIT License
      •1•5•3•2•Updated Mar 24, 2025Mar 24, 2025

    • rkm

      Public
      Generic k-means implementation written in Rust
      Rust
      •9•0•0•0•Updated Mar 20, 2025Mar 20, 2025

    • HumanColonCancer_VisiumHD

      Public
      Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"
      spatial-transcriptomicsvisiumhd
      R
      •
      Other
      •3•56•0•0•Updated Mar 19, 2025Mar 19, 2025

    • rust-shardio

      Public
      Out-of-memory sorting of large datasets map / reduce style processing
      Rust
      •
      MIT License
      •4•47•3•3•Updated Mar 10, 2025Mar 10, 2025

    • enclone

      Public
      VDJ Clonotyping & Analysis Tools
      bioinformatics
      Rust
      •
      Other
      •14•48•4•0•Updated Mar 7, 2025Mar 7, 2025

    • spaceranger

      Public
      Rust
      •
      Other
      •0•2•1•1•Updated Mar 7, 2025Mar 7, 2025

    • image-analysis-rs

      Public
      Rust
      •
      Other
      •0•0•0•1•Updated Mar 7, 2025Mar 7, 2025

    • cellranger

      Public
      10x Genomics Single Cell Analysis
      Rust
      •
      Other
      •95•390•0•0•Updated Feb 11, 2025Feb 11, 2025

    • loupeR

      Public
      Convert Seurat objects to 10x Genomics Loupe files.
      r-package10xgenomicssingle-cell-genomics
      R
      •
      Other
      •15•114•1•0•Updated Feb 5, 2025Feb 5, 2025

    • lz4-rs

      Public
      Rust LZ4 bindings
      Rust
      •
      MIT License
      •79•50•4•1•Updated Jan 7, 2025Jan 7, 2025

    • hdf5-rust

      Public
      HDF5 for Rust
      Rust
      •
      Apache License 2.0
      •94•0•0•3•Updated Jan 2, 2025Jan 2, 2025

    • fastq_set

      Public archive
      Tools for working FASTQ files from sequencers (R1/R2/I1/I2)
      Rust
      •
      Other
      •3•13•0•0•Updated Dec 6, 2024Dec 6, 2024

    • scan-rs

      Public
      Single-cell analysis methods in Rust
      Rust
      •
      Other
      •1•21•1•1•Updated Nov 26, 2024Nov 26, 2024

    • websummary

      Public
      Generate an HTML report in Rust
      Rust
      •
      Other
      •0•5•0•2•Updated Nov 26, 2024Nov 26, 2024

    • FIt-SNE

      Public
      Fast Fourier Transform-accelerated Interpolation-based t-SNE (FIt-SNE)
      C++
      •
      Other
      •107•0•0•1•Updated Oct 26, 2024Oct 26, 2024

    • intel-mkl-src

      Public
      Redistribute Intel MKL as a crate
      Rust
      •
      Other
      •23•0•0•0•Updated Oct 23, 2024Oct 23, 2024

    • fftw

      Public
      FFTW3 binding for Rust
      Rust
      •
      Other
      •28•0•0•1•Updated Oct 22, 2024Oct 22, 2024

    • seurat

      Public
      R toolkit for single cell genomics
      R
      •
      Other
      •941•3•0•0•Updated Sep 29, 2024Sep 29, 2024

    • enclone_ranger

      Public
      Core components for enclone
      Rust
      •
      Other
      •4•4•0•11•Updated Aug 1, 2024Aug 1, 2024

    • rust-debruijn

      Public
      De Bruijn graphs in Rust
      Rust
      •
      MIT License
      •17•66•2•4•Updated Jul 22, 2024Jul 22, 2024

    • rust-boomphf

      Public
      Fast and scalable minimal perfect hashing for massive key sets
      Rust
      •
      MIT License
      •27•139•7•4•Updated Jul 8, 2024Jul 8, 2024

    • zarr

      Public
      Rust implementation of the Zarr N-dimensional array format.
      Rust
      •
      Apache License 2.0
      •5•1•0•1•Updated Jun 28, 2024Jun 28, 2024

    • cell-annotation-service-client

      Public
      Python client libraries for Cellarium Cloud Cell Annotation Service (CAS).
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated May 6, 2024May 6, 2024

    • rust-pseudoaligner

      Public
      Single-Cell RNA-seq pseudo-aligner
      Rust
      •
      MIT License
      •14•51•0•7•Updated May 6, 2024May 6, 2024

    • rust-toolbox

      Public archive
      Rust utility code
      Rust
      •
      MIT License
      •14•32•1•13•Updated Feb 9, 2024Feb 9, 2024

    • subset-bam

      Public
      Rust
      •
      MIT License
      •10•72•15•10•Updated Dec 11, 2023Dec 11, 2023

    • janesick_nature_comms_2023_companion

      Public
      Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue"
      visualizationregistrationvisiuminsitu-dataxenium
      Jupyter Notebook
      •
      Other
      •4•18•1•0•Updated Nov 30, 2023Nov 30, 2023