Velocyto

scVelo — RNA velocity generalized through dynamical modeling. Estimates splicing kinetics from single-cell RNA-seq data using steady-state, stochastic, and dynamical models to infer cellular dynamics,

3 shared topics

The GTEx Pipeline is a standardized RNA-seq processing pipeline for the TOPMed project. It enables reproducible and harmonized analysis of gene expression, generating aligned reads, QC metrics, and bo

2 shared topics

SPOTlight — R/Bioconductor spatial transcriptomics deconvolution using seeded NMF regression. Estimates cell type proportions at each spatial location by integrating single-cell RNA-seq reference data

2 shared topics

Cell Ranger — 10x Genomics official analysis pipeline for Chromium single-cell and spatial data. Performs FASTQ generation, alignment (STAR-based), barcode processing, UMI counting, V(D)J assembly, Fe

1 shared topic • 1 shared operation

EBSeq is an R/Bioconductor package implementing an empirical Bayes hierarchical model for identifying differentially expressed (DE) genes and isoforms in RNA-seq experiments. It supports both two-cond

1 shared topic • 1 shared operation