make_object

A Seurat object is created from the assays, metadata and miscellaneous objects and written to an RDS file.

Inputs

Channel name	Description	Type
`opt`	A map of task-specific variables.	`map`
`tag`	A unique identifier to use in the tag directive.	`string`
`remove barcode suffix`	Whether to remove numeric suffix from barcode (usually “-1”). This should be “TRUE” or “FALSE”.	`string`
`assays`	A list of files that contain assays to include in the object.	`files`
`assay names`	A list of names that the assays should be saved to in the object. Must be the same order as `assays`.	`strings`
`misc data`	A list of files that contain objects that should be added to the `misc` slot of the Seurat object.	`files`
`misc names`	A list of names that the miscellaneous objects should be saved to in the object. Must be the same order as `misc data`.	`strings`
`project`	The name of the dataset to save in the object, accessed via `Seurat::Project()`.	`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`
`seurat`	A Seurat object with assays and miscellaneous objects.	`file`	`seurat.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.

DOI Homepage Documentation Source