10x Genomics

cellranger

10x Genomics Single Cell Analysis

vartrix

Single-Cell Genotyping Tool

rust-boomphf

Fast and scalable minimal perfect hashing for massive key sets

loupeR

Convert Seurat objects to 10x Genomics Loupe files.

subset-bam

rust-debruijn

De Bruijn graphs in Rust

bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines

rust-pseudoaligner

Single-Cell RNA-seq pseudo-aligner

rust-shardio

Out-of-memory sorting of large datasets map / reduce style processing

enclone

VDJ Clonotyping & Analysis Tools

lz4-rs

Rust LZ4 bindings

rust-toolbox

Rust utility code

HumanColonCancer_VisiumHD

Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"

orbit

Rust wrapper for STAR aligner

scan-rs

Single-cell analysis methods in Rust

fastq_set

Tools for working FASTQ files from sequencers (R1/R2/I1/I2)

janesick_nature_comms_2023_companion

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"

analysis_guides

10x Genomics analysis guides files

websummary

Generate an HTML report in Rust

clippy-check

📎 GitHub Action for PR annotations with clippy warnings

enclone_ranger

Core components for enclone

gpython

gpython is a python interpreter written in go "batteries not included"

seurat

R toolkit for single cell genomics

cell-annotation-service-client

Python client libraries for Cellarium Cloud Cell Annotation Service (CAS).

hdf5-rust

HDF5 for Rust

intel-mkl-src

Redistribute Intel MKL as a crate

ndarray-linalg

Linear algebra package for rust-ndarray using LAPACK binding

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

simple_excel_writer

simple excel writer in Rust

zarr

Rust implementation of the Zarr N-dimensional array format.