import_scseq: Import raw single cell fastq or cellranger files for app

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

Import raw single cell fastq or cellranger files for app

Description

Import raw single cell fastq or cellranger files for app

Usage

import_scseq(
  dataset_name,
  uploaded_data_dir,
  sc_dir,
  tx2gene_dir,
  species = NULL,
  progress = NULL,
  value = 0,
  founder = dataset_name,
  npcs = 30,
  cluster_alg = "leiden",
  resoln = 1,
  ref_name = NULL,
  metrics = c("low_lib_size", "low_n_features", "high_subsets_mito_percent",
    "low_subsets_ribo_percent", "high_doublet_score")
)

Arguments

dataset_name	Name of dataset
uploaded_data_dir	Directory with fastq or cellranger files
sc_dir	Single cell directory for app. Will store results in dataset_name subdirectory
tx2gene_dir	Path to directory containing transcript to gene maps produced by load_tx2gene.
species	Name of species. Used for R object imports only (detected for cellranger files).
progress	Optional shiny Progress object. Default will print progress.
value	Integer indicating step of pipeline.
founder	Name of dataset that dataset_name originates from.

hms-dbmi/drugseqr documentation built on Feb. 15, 2024, 10:38 p.m.