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.
Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)
simplified cellranger for long-read data
Standalone tool and library allowing to work with barcoded linked-reads
Collection of tools and resources for linked-reads
Sanger Cellular Genetics single-cell ATAC-seq pipeline.
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, subtyp…
De novo assembly pipeline for 10X linked-reads using Supernova
R script built on Seurat objects to analyze 10X single-cell expression data
Pipeline for SV detection using 10X genomics data
Preliminary study to figure out how many larval gonads are needed for RNA-Seq
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
Download fastqs or supplementary files from GEO and upload to hca-util bucket
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