10XGenomics/janesick_nature_comms_2023_companion

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10XGenomics/janesick_nature_comms_2023_companion

10XGenomics

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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"

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.

single-cell-3prime-paper

subset-bam

supernova

10x Genomics Linked-Read Diploid De Novo Assembler

rust-debruijn

De Bruijn graphs in Rust

bamtofastq

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

scHLAcount

Count HLA alleles in single-cell RNA-seq data

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

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"

longranger

10x Genomics Linked-Read Alignment, Variant Calling, Phasing, and Structural Variant Calling

lariat

Linked-Read Alignment Tool

single-cell-3prime-snp-clustering

rust-bwa

Rust wrapper of the BWA C API

cellranger-atac

scan-rs

Single-cell analysis methods in Rust

fastq_set

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

orbit

Rust wrapper for STAR aligner

thermite

Spliced short read aligner implemented in Rust

websummary

Generate an HTML report in Rust

analysis_guides

10x Genomics analysis guides files

Jupyter Notebook

enclone_ranger

Core components for enclone

supernova-chili-pepper

rules_conda

Bazel rules for creating conda environments

louvain

Louvain graph clustering

cellranger-dna

Single Cell DNA Copy Number Profiling