loompy

CytoTRACE -- computational method for predicting relative differentiation state of cells from single-cell RNA-seq data. Uses gene counts (number of detectably expressed genes per cell) as a robust pro

2 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 • 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

2 shared topics • 1 shared operation

Salmon is an ultrafast, bias-correcting tool for quantifying transcript abundances from RNA-seq reads using quasi-mapping or selective alignment. Alevin is Salmon's single-cell mode for generating cel

2 shared topics • 1 shared operation

Scrublet — Python toolkit for computational identification of cell doublets in single-cell RNA-seq data. Simulates synthetic doublets from observed transcriptomes and scores cells via k-nearest-neighb

2 shared topics • 1 shared operation