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10X_Chromium_3prime_Data

README.md

GeneLab bioinformatics processing pipeline for 10X Chromium 3' single cell RNA-sequencing data

The document GL-DPPD-7111.md holds an overview and example commands for how GeneLab processes single cell RNA-sequencing (scRNAseq) datasets. See the Repository Links descriptions below for more information. Processed data output files and a GeneLab data processing summary is provided for each GLDS dataset in the Open Science Data Repository (OSDR).

Repository Links

  • Pipeline_GL-DPPD-7111_Versions

    • Contains the current and previous GeneLab single cell RNAseq consensus processing pipeline (scRCP) versions documentation

  • GeneLab_CellType_GeneMarkers

    • Contains the species and tissue specific cell type gene markers GeneLab uses for cell annotations for the current and previous GeneLab scRCP versions

  • scRNAseq_Tool_Install

    • Contains instructions and associated yaml files to install the conda environments containing tools used to process single cell RNAseq datasets using the GeneLab scRCP

Developed and maintained by:

Lauren Sanders
Amanda Saravia-Butler