Human Cell Atlas Tools

Use when working with EmptyDrops or DropletUtils — the Bioconductor R package for distinguishing real cells from empty droplets in droplet-based single-cell RNA-seq data (10x Genomics, Drop-seq, inDro

3 shared topics • 1 shared operation

CopyKAT (Copy number Karyotyping of Tumors) — R package for inferring genome-wide aneuploidy and copy number variations from single-cell RNA-seq data. Uses Bayesian segmentation to distinguish tumor (

3 shared topics

WARP (WDL Analysis Research Pipelines) — Broad Institute's cloud-optimized collection of genomics pipelines written in WDL (Workflow Description Language). Covers whole-genome sequencing (WGS), whole-

3 shared topics

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

salmon — Fast, bias-aware transcript quantification from RNA-seq data using selective alignment to the transcriptome. Supports bulk RNA-seq (mapping-based and alignment-based modes), single-cell RNA-s

3 shared topics