DESeq2 pairwise differential analysis

TASK

Typing name : TASK.gws_omix.DESeq2DifferentialAnalysis

Brick : gws_omix

Compute differential analysis using DESeq2 R package (pairwise comparison)

DESeq2DifferentialAnalysis class.

Salmon_merged_counts

Salmon merged raw count files

Metadata_file

Metadata file describing samples (see https://hub.gencovery.com/bricks/gws_omix/latest/doc/use-cases/undefined )

Deseq2 output files

DEseq2 output tables containing fold-change and statistics

Deseq2 output folder

DEseq2 output folder containing all output files

Deseq2 summary file

DEseq2 output file which summarise under the threshold genes differentially expressed

metadata_column

Optional

Column on which the differential analysis will be performed

Type : string

output_file_names

Optional

Choose the output file names (e.g. output_file --> output-file.XXX.txt, ...)

Type : string

Default value : DESeq2

summary_threshold

Optional

Choose the threshold used to filter adjusted p-value to generate summary file

Type : float

Default value : 0.05