make_chromatin_assay
Create a chromatin assay using Signac and a counts matrix.
moduleInputs
| Channel name | Description | Type |
|---|---|---|
opt | A map of task-specific variables. | map |
tag | An identifier to use in the tag directive. | string |
annotations | GRanges object of GTF save as RDS file. | file |
counts matrices | RDS file of the counts matrices loaded by Seurat. | file |
quantification path | Path to the quantified dataset from which the ATAC-seq fragments are read. | path |
feature type | The name of the list key in counts matrices that contains the chromatin assay data (eg. “Chromatin Accessibility”). | 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 |
assay | RDS file of the newly created chromatin accessibility assay. | file | assay.rds |
Tools
r
R is a free software environment for statistical computing and graphics.
Homepage Documentationsignac
Signac is designed for the analysis of single-cell chromatin data, including scATAC-seq, single-cell targeted tagmentation methods such as scCUT&Tag and scNTT-seq, and multimodal datasets that jointly measure chromatin state alongside other modalities.
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