import_plate_txis: import plate-seq velocity information (from Salmon) to a...

In trichelab/velocessor: The world's dumbest single-cell RNA velocity calculator and loader

Description

Automated (more or less) importation of STORM-seq and SMART-seq123 data for downstream attempts at merging with droplet data, index sort visualization, and so forth.

Usage

import_plate_txis(
  quants,
  t2g = NA,
  type = "salmon",
  gtf = NULL,
  qc = TRUE,
  fixrn = TRUE,
  ...
)

Arguments

quants	where the quant.sf files are
t2g	required file with tx2gene information for TPM calcs
type	What type of quantifications are these? ("salmon")
gtf	Where an expanded GTF lives if not collapsed to gene-level
qc	Whether QC should be performed to toss low-quality cells
fixrn	Fix goofy versioned ENSEMBL gene names? (TRUE)
...	additional parameters to pass to tximport, if any

Details

FIXME: Add Kallisto support and Arkas style txome/repeatome/spikeome support. FIXME: Add in ability to support bootstraps/Gibbs samples from salmon

Value

     A SingleCellExperiment with 'spliced' & 'unspliced' assays.

trichelab/velocessor documentation built on Jan. 5, 2022, 6:27 p.m.