CUT&RUN and CUT&Tag data processing and analysis

Cluster-specific pseudo-bulk analysis of 10X single-cell RNA-seq data by connecting Seurat to the VBC RNA-seq pipeline.

⚪ ➡️ 🔍 ℹ️ A suggested workflow, and accompanying scripts, to assemble Single Amplified Genomes (SAGs) from MDA derived Hi/MiSeq (Overlapped) Paired-End Illumina Libraries.

Single Cell Allele-Specific Analysis - Containerized tool for genotyping, phasing, mapping bias correction, and generation of single cell allele-specific counts

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.

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

A suggested workflow, and accompanying scripts, to assemble Single Amplified Genomes (SAGs) from MDA derived Hi/MiSeq (Overlapped) Paired-End Illumina Libraries.

Salmon Alevin (single cell) quantification wrapper module for GenePattern.

10x Cell Ranger Docker Image

Single Cell Journalling

Dockerized Cell Ranger ATAC

Downloading and processing pipelines used for single cell gene expression assays of human tumor biopsies

For analysis of Visium and Nanopore matched spatial and long read sequencing

V(D)J T Cell and B Cell Analysis with cellranger vdj