OneK1K Tools

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 • 2 shared operations

Use when working with ArchR for single-cell chromatin accessibility (scATAC-seq) analysis in R. ArchR builds Arrow-backed projects from fragment/BAM inputs, performs doublet scoring, iterative LSI, cl

2 shared topics • 3 shared operations

CellBender removes ambient RNA contamination and technical noise from droplet-based single-cell RNA-seq data using a deep generative model (VAE). Processes raw 10x Genomics feature-barcode matrices to

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 • 1 shared operation

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 • 1 shared operation