Firecloud / WARP Pipelines

cellSNP-lite — fast C-based tool for genotyping single cells and bulk samples at known or de-novo SNP sites from BAM/SAM files. Generates sparse genotype matrices (AD/DP/OTH counts) in VCF/BCF format

3 shared topics • 1 shared operation

FLAMES — Full-Length Analysis of Mutations and Splicing for bulk and single-cell long-read RNA-seq data. R/Bioconductor pipeline for barcode demultiplexing, isoform discovery, transcript quantificatio

3 shared topics • 1 shared operation

Loom — HDF5-based file format and Python library (loompy) for storing and accessing large single-cell RNA-seq datasets. Supports sparse/dense matrices, row attributes (genes/features), column attribut

3 shared topics • 1 shared operation

Use when working with OneK1K tools from the Powell Genomics Lab — the single-cell eQTL (sc-eQTL) analysis suite built around the OneK1K cohort (~1.27 million PBMCs from 982 donors). Covers the full pi

3 shared topics • 1 shared operation

Pegasus is a Python package for analyzing and visualizing large-scale single-cell and single-nucleus RNA-seq data, developed by the Broad Institute's Li Lab. Performs QC filtering, normalization, PCA,

3 shared topics • 1 shared operation