openCyto

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

3 shared topics • 2 shared operations

Use this skill for SCTransform normalization of single-cell RNA-seq count matrices. Route here when users ask about variance stabilizing transformation (VST), regularized negative binomial regression

3 shared topics • 2 shared operations

Splatter is an R/Bioconductor package for simulating single-cell RNA-seq (scRNA-seq) count data. Use when users need to generate synthetic scRNA-seq datasets for benchmarking clustering, trajectory, o

3 shared topics • 2 shared operations

SymSim is an R package for simulating single-cell RNA sequencing (scRNA-seq) data using a mechanistic two-stage kinetic model. Use when users need to generate realistic synthetic scRNA-seq datasets wi

3 shared topics • 2 shared operations

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

3 shared topics • 1 shared operation