Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

• UpdatedMar 11, 2025
• Nextflow

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

• UpdatedApr 20, 2021
• R

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

• UpdatedFeb 8, 2019

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

• UpdatedMar 14, 2025
• Nextflow

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

• UpdatedMay 6, 2019
• R

simplified cellranger for long-read data

• UpdatedSep 18, 2024
• Python

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

• UpdatedDec 7, 2024
• C++

Collection of tools and resources for linked-reads

• UpdatedDec 17, 2024

Sanger Cellular Genetics single-cell ATAC-seq pipeline.

• UpdatedAug 25, 2023
• Nextflow

Perform Visium Standard Definition (SD) spot deconvolution into putative single cells using distance-based gene clustering and cell type formulation.

• UpdatedMar 11, 2025
• Jupyter Notebook

CWL toolkit for single-cell sequencing data analysis

• UpdatedNov 11, 2022
• Common Workflow Language

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…

• UpdatedOct 7, 2020
• R

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

• UpdatedSep 15, 2020
• Nextflow

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

• UpdatedDec 14, 2021
• R

Pipeline for SV detection using 10X genomics data

• UpdatedOct 8, 2018
• Python

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

• UpdatedAug 5, 2020
• Jupyter Notebook

Cloupe reader

• UpdatedJan 13, 2025
• Python

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

• UpdatedJun 21, 2019
• C++

Scripts developed to work with 10x Genomics sequencing results

• UpdatedSep 20, 2017
• R

Paper list of single cell omics

• UpdatedAug 27, 2019