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

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

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

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

No description provided.

simplified cellranger for long-read data

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

Sanger Cellular Genetics single-cell ATAC-seq pipeline.

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

Collection of tools and resources for linked-reads

Optimized pipelines for Spatial Transcriptomics (ST) data analysis using Seurat & Giotto, designed for reproducible benchmarking and biological insight.

Computational biology/bioinformatics workflows, codes, tech & concept notes on NGS data

Perform Visium Standard Definition (SD) cell type-specific gene expression reconstruction via spot deconvolution.

Cloupe reader

CWL toolkit for single-cell sequencing data analysis

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, subtype, cell state, cluster number etc). This package is best suited for researchers who want to annotate their datasets in a quick and unbiased way, phenotype their datasets based on cell identity proportions, and discover common cell states across different datasets and disease models.

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

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

G00x - Generalizable Germline-Targeting Clinical Trial Pipeline

Pipeline for SV detection using 10X genomics data

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

This repository provides an end-to-end workflow for variant calling from single-cell RNA-seq data (scRNA-seq) using Cell Ranger, custom Python BAM splitting, and cellsnp-lite. The pipeline works with 10x Genomics and Drop-seq data and supports human and mouse genomes.

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

Scripts developed to work with 10x Genomics sequencing results

Paper list of single cell omics

No description provided.

A complete single-cell RNA-seq analysis pipeline using Scanpy on 10x Genomics PBMC data, including clustering, UMAP visualization, and marker gene detection.

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

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

Convert your STDeconvolve-generated and EnrichR-decoded topics into Seurat spatial clustering information via AUCell