CellBender

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

3 shared topics • 2 shared operations

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

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

Use when performing single-cell QTL (sc-eQTL, sc-sQTL) mapping with SAIGE-QTL. SAIGE-QTL extends the SAIGE framework to single-cell RNA-seq data using Poisson mixed models to handle count overdispersi

3 shared topics • 1 shared operation

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 • 1 shared operation