differential_expression/deseq2

Description

Performs differential expression analysis using DESeq2 on bulk samples or pseudobulk samples aggregated from single-cell data.
Note that this component only considers factors as explanatory variables, and excludes covariates from the analysis.

Type

r_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
p_adj_threshold: [ 0.05 ]  
log2fc_threshold: [ 0 ]  
output_dir: "$id.$key.output_dir"  
output_prefix: [ "deseq2_analysis" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.1 \  
  -main-script target/nextflow/differential_expression/deseq2/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input h5mu file containing (pseudo-)bulk transcriptomic samples.
--modality	string	Which modality from the input MuData file to process.
--input_layer	string	Input layer to use. If None, X is used. This layer must contain raw counts.
--var_gene_names	string	Name of the .var field that contains gene symbols. If not provided, .var.index will be used.
--obs_cell_group	string	.obs field containing the cell group information, for example per cell type or per cell cluster. If true, performs per-cell-group analysis with cell-group-specific results.

Name

Type & Properties

--input

-i

file

required

--modality

string

--input_layer

string

--var_gene_names

string

--obs_cell_group

string

Arguments

Name	Type & Properties	Description
--design_formula	string required	The formula should be a tilde (~) followed by the variables with plus signs between them. The design formula is used to estimate the dispersions and to estimate the log2 fold changes of the model.
--contrast_column	string required	Column in the metadata to use for the contrast. This column should contain the conditions to compare.
--contrast_values	string required multiple	Values to compare in the contrast column. First value is the control group, following values are comparison groups. Values must be present in the fields specified for the design formula.
--p_adj_threshold	double	Adjusted p-value threshold for significance, corrected with the Benjamini and Hochberg method. Genes with adjusted p-values below this threshold will be considered significant.
--log2fc_threshold	double	Log2 fold change threshold for significance. Genes with absolute log2 fold change above this threshold will be considered significant.

Name

Type & Properties

--design_formula

string

required

--contrast_column

string

required

--contrast_values

string

required

multiple

--p_adj_threshold

double

--log2fc_threshold

double

Outputs

Name	Type & Properties	Description
--output_dir -o	file required output	Output directory for DESeq2 results. If cell groups are defined (using `--obs_cell_group`), the output folder will contain one CSV per cell group, otherwise it will contain a single output file.
--output_prefix	string	Prefix for output CSV files. If no cell groups are specified, the output file will be named "{prefix}.csv". If cell groups are specified, files will be named "{prefix}_{cell_group}.csv".

Name

Type & Properties

--output_dir

-o

file

required

output

--output_prefix

string