SeuratToCoNGA: SeuratToCoNGA

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

SeuratToCoNGA

Description

A wrapper function to prepare a Seurat object for Conga.

Usage

SeuratToCoNGA(seuratObj, tcrClonesFile, seuratToCongaDir, assayName = "RNA")

Arguments

seuratObj	The Seurat object to be written into a 10x file format
tcrClonesFile	The 10x clonotypes file for this Seurat object. Single lanes can use the CellRanger/Vloupe contigs CSV file. Merged lanes need to merge these files and modify them to create unique cellbarcodes and clonotype names, such as the code from Rdiscvr::CreateMergedTcrClonotypeFile().
seuratToCongaDir	The local path to write the output files.
assayName	The name of the gene expression data assay.

bimberlabinternal/CellMembrane documentation built on Dec. 25, 2024, 8:10 a.m.