CellPhoneDB

BPCells is a high-performance toolkit for large single-cell RNA-seq and ATAC-seq datasets. Use it when the user mentions BPCells, disk-backed sparse matrices, bitpacked single-cell storage, large 10x

3 shared topics • 2 shared operations

scde is a Bioconductor R package for Bayesian single-cell differential expression analysis using mixture models. It fits a per-cell error model (negative binomial + Poisson noise) to raw count data, t

3 shared topics • 1 shared operation

DecontX — R/Bioconductor method in the celda package for estimating and removing ambient RNA contamination from droplet-based single-cell RNA-seq data. Uses a Bayesian Dirichlet mixture model over cel

2 shared topics • 2 shared operations

Leafcutter — annotation-free RNA splicing quantification from short-read RNA-seq data. Detects differential intron usage, alternative splicing events, outlier splicing (LeafcutterMD), and splicing QTL

2 shared topics • 2 shared operations

Palantir — pseudotime and cell fate probability analysis for single-cell RNA-seq data using Markov diffusion chains. Computes a continuous pseudotime ordering from a user-specified start cell and quan

2 shared topics • 2 shared operations