AnnData

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 • 2 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

2 shared topics • 2 shared operations

Cellranger-arc — 10x Genomics pipeline for processing Multiome ATAC + Gene Expression data from the Chromium Multiome kit. Aligns FASTQ reads, calls peaks, quantifies gene expression and chromatin acc

2 shared topics • 2 shared operations

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

2 shared topics • 2 shared operations

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,

2 shared topics • 2 shared operations