write_10x_counts_matrices

Reads a directory containing Cell Ranger-formatted output into a list of matrices.

Inputs

Channel name	Description	Type
`opt`	A map of task-specific variables.	`map`
`tag`	A unique identifier to use in the tag directive.	`string`
`barcoded_matrix`	Path to the Cell Ranger-formatted (probably filtered) output files.	`path`
`feature_identifier`	Either “accession” or “name” to indicate which type of feature identifier should be used. For example, in a gene expression context “accession” may be Ensembl identifiers and “name” could be gene names.	`string`

Outputs

Emission name	Description	Type	Filename pattern
`opt`	A map of task-specific variables.	`map`
`task`	YAML-formatted file of task parameters and software versions used by the task.	`file`	`task.yaml`
`counts_matrices`	An RDS file of a list of counts matrices, provided by `Seurat::Read10X()`.	`file`	`counts_matrices.rds`
`features`	A data frame containing the accession and names of features.	`file`	`features.rds`

Tools

r

R is a free software environment for statistical computing and graphics.

Homepage Documentation

seurat

Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.

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