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    69 repositories

    • 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
      •2•39•0•1•Updated Nov 18, 2024Nov 18, 2024

    • orbit

      Public
      Rust wrapper for STAR aligner
      C
      •
      MIT License
      •2•15•0•5•Updated Nov 18, 2024Nov 18, 2024

    • rules_conda

      Public
      Bazel rules for creating conda environments
      condabazel-rulesconda-environmentbazel-deps
      Go
      •
      MIT License
      •1•3•3•1•Updated Nov 18, 2024Nov 18, 2024

    • analysis_guides

      Public
      10x Genomics analysis guides files
      Jupyter Notebook
      •10•6•0•0•Updated Nov 13, 2024Nov 13, 2024

    • hdf5-rust

      Public
      HDF5 for Rust
      Rust
      •
      Apache License 2.0
      •86•0•0•3•Updated Nov 12, 2024Nov 12, 2024

    • loupeR

      Public
      Convert Seurat objects to 10x Genomics Loupe files.
      r-package10xgenomicssingle-cell-genomics
      R
      •
      Other
      •15•100•0•0•Updated Oct 29, 2024Oct 29, 2024

    • FIt-SNE

      Public
      Fast Fourier Transform-accelerated Interpolation-based t-SNE (FIt-SNE)
      C++
      •
      Other
      •108•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
      •27•0•0•1•Updated Oct 22, 2024Oct 22, 2024

    • fastq_set

      Public
      Tools for working FASTQ files from sequencers (R1/R2/I1/I2)
      Rust
      •
      Other
      •3•14•0•11•Updated Sep 30, 2024Sep 30, 2024

    • seurat

      Public
      R toolkit for single cell genomics
      R
      •
      Other
      •917•2•0•0•Updated Sep 29, 2024Sep 29, 2024

    • lz4-rs

      Public
      Rust LZ4 bindings
      Rust
      •
      MIT License
      •76•47•4•1•Updated Sep 26, 2024Sep 26, 2024

    • rust-shardio

      Public
      Out-of-memory sorting of large datasets map / reduce style processing
      Rust
      •
      MIT License
      •4•47•3•1•Updated Sep 6, 2024Sep 6, 2024

    • enclone

      Public
      VDJ Clonotyping & Analysis Tools
      bioinformatics
      Rust
      •
      Other
      •14•47•4•2•Updated Sep 3, 2024Sep 3, 2024

    • cellranger

      Public
      10x Genomics Single Cell Analysis
      Rust
      •
      Other
      •94•366•0•0•Updated Sep 3, 2024Sep 3, 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•63•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•132•5•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

    • scan-rs

      Public
      Single-cell analysis methods in Rust
      Rust
      •
      Other
      •1•14•1•1•Updated Jun 13, 2024Jun 13, 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•50•0•7•Updated May 6, 2024May 6, 2024

    • websummary

      Public
      Generate an HTML report in Rust
      Rust
      •
      Other
      •0•5•0•2•Updated Mar 20, 2024Mar 20, 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•69•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
      •3•15•1•0•Updated Nov 30, 2023Nov 30, 2023

    • bamtofastq

      Public
      Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
      Rust
      •
      MIT License
      •6•59•16•8•Updated Nov 20, 2023Nov 20, 2023

    • vartrix

      Public
      Single-Cell Genotyping Tool
      Rust
      •
      MIT License
      •26•199•27•10•Updated Oct 2, 2023Oct 2, 2023

    • ndarray-linalg

      Public
      Linear algebra package for rust-ndarray using LAPACK binding
      Rust
      •
      Other
      •76•1•0•0•Updated Sep 19, 2023Sep 19, 2023

    • clippy-check

      Public
      📎 GitHub Action for PR annotations with clippy warnings
      TypeScript
      •
      MIT License
      •42•3•0•3•Updated Jul 9, 2023Jul 9, 2023