A single-cell RNAseq pipeline for 10X genomics data

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

De novo assembly pipeline for 10X linked-reads using Supernova

Sanger Cellular Genetics single-cell ATAC-seq pipeline.

Standalone tool and library allowing to work with barcoded linked-reads

simplified cellranger for long-read data

Pipeline for SV detection using 10X genomics data

Collection of tools and resources for linked-reads

R package: {rfca} Random forest-based cell annotation methods for scRNAseq analysis. {rfca} contains methods which identifies cell types using machine learning trained on a diversity of cell types, without the need for a labelled training dataset. It also allows you to train your own cell prediction models with your own labels (cell type, subtyp…

Preliminary study to figure out how many larval gonads are needed for RNA-Seq

Download fastqs or supplementary files from GEO and upload to hca-util bucket

Cloupe reader

CWL toolkit for single-cell sequencing data analysis

R script built on Seurat objects to analyze 10X single-cell expression data

Single-cell preprocessing pipelines, such as converting raw bcl files, make fastqs and then generating quantified matrix, etc

adtseq provides simple Rcpp methods to identify Antibody-Derived-Tags in single cell CITE/REAP-seq data