Sessions Reports and Methods Text

Sessions, reports and methods text

Sessions

Save session writes a JSON file containing the analysis state: sample inclusion, group assignments and order, design type, normalization, filter, DE method, contrast and thresholds, covariates, font scale, annotation choice and Discovery settings. The file does not contain the expression data. To restore, load the same data files, then Load session.

The file records the application version. Loading a session saved by a different version displays a warning, because defaults or methods may have changed.

Methods text

The Overview & QC tab contains Auto-generated methods text, which describes the analysis as performed: input dimensions, filter, normalization, methods, thresholds, covariates, gene-set tests and cross-dataset procedures, each with its citation. It updates when settings change. Copy it after the final analysis.

Report

Generate report writes a single self-contained HTML file with the settings, sample table, DE summary and top genes, figures, Discovery results, methods text and references.

DESeq2 companion script

DESeq2 script (R) writes an R script for the current contrast and sample selection, for users who want a DESeq2 analysis of the same data.