SummarizedExperiment

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

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

1 shared topic • 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

1 shared topic • 1 shared operation

gffread -- GFF/GTF utility for filtering, converting, and extracting sequences from genome annotation files. Converts between GFF3 and GTF formats, extracts transcript (FASTA) and protein sequences fr

1 shared topic • 1 shared operation

IsoformSwitchAnalyzeR — R/Bioconductor package for detecting, annotating, and visualizing isoform switches with functional consequences from RNA-seq data. Integrates with Salmon, kallisto, StringTie,

1 shared topic • 1 shared operation