Open Source Code
RNA-seq Analytic Pipeline for GUDMAP/RBK
This pipeline conducts end-to-end RNA-seq analysis on replicates stored in the GenitoUrinary Development Molecular Anatomy Project and ReBuilding the Kidney consortium. This pipeline was created in a collaboration between the Strand Lab and Bioinformatics Core Facility (BICF) at UT Southwestern Medical Center.This pipeline conducts end-to-end RNA-seq analysis on replicates stored in the GenitoUrinary Development Molecular Anatomy Project and ReBuilding the Kidney consortium. This pipeline was created in a collaboration between the Strand Lab and Bioinformatics Core Facility (BICF) at UT Southwestern Medical Center.
Strand Lab analysis of single-cell RNA sequencing
This code was used for the single-cell RNA-sequencing analysis in the Strand Lab at UT Southwestern Medical Center
Single-Cell RNA-Seq Image Generation Pipeline for GUDMAP/RBK
This pipeline takes a Seurat object containing single-cell RNA-sequencing data and generates all the plots required to explore the data without querying the data directly. This pipeline was primarily written for uploading the outputs to GenitoUrinary Development Molecular Anatomy Project and ReBuilding the Kidney project. This pipeline was created in a collaboration between the Strand Lab and Bioinformatics Core Facility (BICF) at UT Southwestern Medical Center.
BICF Cellranger mkfastq Analysis Workflow
BICF Cellranger mkfastq Analysis Workflow is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illumina's bcl2fastq). This pipeline, used by the Bioinformatics Core Facility at UT Southwestern, demultiplexes samples from 10x Genomics single-cell libraries into fastqs. FastQC is run on the results all reports are collated with the MultiQC tool. This pipeline is primarily used with a SLURM cluster on BioHPC, but it should be able to run on any system that Nextflow supports. Additionally, this pipeline is designed to work using a simple web interface.
BICF Cellranger count Analysis Workflow
BICF Cellranger count Analysis Workflow is a wrapper for the cellranger count tool from 10x Genomics. This pipeline, used by the Bioinformatics Core Facility at UT Southwestern, takes fastq files from 10x Genomics single-cell gene expression libraries and passes them to cellranger count, managing parallelization of multiple runs, as well as, aggregation as appropriate. This pipeline is primarily used with a SLURM cluster on BioHPC, but it should be able to run on any system that Nextflow supports. Additionally, this pipeline is designed to work using a simple web interface.
Determining cellular heterogeneity in the human prostate with single-cell RNA sequencing
This is the code which was used for the single-cell RNA-sequencing analysis published in Cell Reports 2018 and used the data in GenitoUrinary Development Molecular Anatomy Project