10XGenomics/analysis_guides

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10XGenomics/analysis_guides

10XGenomics

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10x Genomics analysis guides files

cellranger

10x Genomics Single Cell Analysis

vartrix

Single-Cell Genotyping Tool

rust-boomphf

Fast and scalable minimal perfect hashing for massive key sets

single-cell-3prime-paper

loupeR

Convert Seurat objects to 10x Genomics Loupe files.

subset-bam

rust-debruijn

De Bruijn graphs in Rust

supernova

10x Genomics Linked-Read Diploid De Novo Assembler

scHLAcount

Count HLA alleles in single-cell RNA-seq data

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

rust-toolbox

Rust utility code

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

orbit

Rust wrapper for STAR aligner

fastq_set

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

scan-rs

Single-cell analysis methods in Rust

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"

Jupyter Notebook

thermite

Spliced short read aligner implemented in Rust

websummary

Generate an HTML report in Rust

enclone_ranger

Core components for enclone

supernova-chili-pepper

louvain

Louvain graph clustering

cellranger-dna

Single Cell DNA Copy Number Profiling