IsoQuant: Quantifies full-length isoforms in sample(s)

In noush-joglekar/scisorseqr: Processes long reads for differential isoform analysis

Quantifies full-length isoforms in sample(s)

Description

Depending on whether you want to do downstream differential expression analysis of full-length isoforms, TSS, or PolyA sites, this function annotates and counts up transcripts expressed in the given set of samples

Usage

IsoQuant('AllInfo',Iso=TRUE, TSS=FALSE, PolyA=FALSE)

Arguments

Iso	Logical indicating whether to conduct analysis for full-length isoforms. Defaults to TRUE
TSS	OPTIONAL logical indicating whether to conduct analysis for transcription start sites (TSS). Defaults to FALSE
PolyA	OPTIONAL logical indicating whether to conduct analysis for end sites (PolyA). Defaults to FALSE
AllInfo	Merged file of Gene, Barcode, UMI, Cluster, and transcript across samples and replicates. Major isoform is calculated based on the entire input.

Value

IsoQuantOutput folder containing all useful files for downstream analysis

See Also

DiffSplicingAnalysis

noush-joglekar/scisorseqr documentation built on March 18, 2023, 8:06 p.m.