This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles)
This image is a modular pipeline that facilitates the usage g:Profiler, PANTHER and GSEA for streamlined Enrichment Analysis. Includes support features for input building and output processing.
The documentation is available here
First you need to have Docker installed in your computing environment. If you don't, follow the installation guidelines at pegi3s Bioinformatics Docker Images Project website: http://bdip.i3s.up.pt/
To pull the docker image you should run the following command:
docker pull pegi3s/auto-enrich
To run an analysis you must set up the pipeline configuration file, name it config and have in a folder alongside one, or more, input data file/s (such as a Gene Expression matrix, Genes Lists, GSEA Preranked lists, Gene Sets, etc.) under the /your/data/directory in order for the pipeline to properly work.
Detailed instructions are given in the documentation, where the available modules and parameters to be configured are described in detail.
After setting the require files you should adapt and run the following command:
docker run --rm -v /your/data/directory:/data pegi3s/auto-enrich
In this command, you should replace /your/data/directory to point to the folder that contains the input files for the pipeline.
In either of the following test dataset, the input files are pre-configured inside the /inputs directory and the expected output inside the /outputs directory.
To run the pipeline you should adapt and run following command: docker run --rm -v /your/data/directory:/data pegi3s/auto-enrich
In this command, you should replace /your/data/directory to point to the directory that contains the input files for the pipeline.
This test demonstrates how the auto-Enrich pipeline can be run using all modules to perform Over-Representation Analysis (ORA; with g:Profiler and PANTHER) and Gene Set Enrichment Analysis (GSEA).
The input includes a Gene Expression matrix from Mus musculus, the necessary configuration files, and two gene set files from the Mouse Collections of Molecular Signature DataBase (MSigDB).
Test files: test_data.zip
Contents inside the inputs directory of test_data.zip:
- expression_matrix.tsv: Gene expression data matrix (Gene ID and respective gene expression samples data, from Nogueira-Rodrigues et al. (2022) https://www.researchgate.net/publication/357595784).
- config: Pipeline configuration file, setup to run input file generation for ORA and GSEA methods (Modules 1, 2, and 5), enrichment analysis (Modules 3, 4, and 6) on pre-selected sources, and output processing (Module 7).
- /gene_sets: Folder holding the Gene Sets from the MSigDB to be provided to the GSEA runs (includes the Reactome Pathways gene set: m2.cp.reactome.v2026.1.Mm.symbols.gmt; and the Gene Ontology gene set: m5.go.v2026.1.Mm.symbols.gmt)
Pipeline behaviour workflow (tools="1,2,3,4,5,6,7"):
1. The gene expression matrix is processed to build a genes list (from column index set in the variable gene) of the pre-selected differentially expressed genes marked (1) at the column index (set in the variable selected) [Module 1]
2. The given input gene identifiers are mapped to GeneID, UniProtKBs, HUGO Gene Symbol and Full Name [Module 2]
3. Over-Representation Enrichment Analysis are perfomed, with the mapped genes list, using g:Profiler g:GOSt tool on selected annotations-sources (set in the variable gprofiler_dbs), outputs are processed and enriched terms annotations are mapped [Module 3]
4. Over-Representation Enrichment Analysis are perfomed, with the mapped genes list, using PANTHER Overrepresentation test on selected annotations-sources (set in the variable panther_dbs), outputs are processed and enriched terms annotations are mapped [Module 4]
5. The gene expression matrix is partitioned into scoring Preranked Genes lists (.rnk) by calculating the set fold-changes (in the variables preranked1; preranked2) between computed experimental groups averages (set with the variables number_groups, number_samples, samples, groups, calculate_averages, isoform) [Module 5]
6. Preranked Gene Set Enrichment Analysis (GSEA) are executed using the previously generated Preranked Genes lists with set paramters (method, gene_set, nperm, others set by default) [Module 6]
7. The enrichment results from the different tools are intersected to find common results (intersection boolean variable) and individual tool results are filtered (by set variable max_annot; maximum allowed enriched term size ) [Module 7]
Output directories after the run:
# Generated inputs for Enrichment Analysis
/data/
├── annotations/* → Utilized sources to map gene identifiers and terms annotations
├── preranked_gene_lists/
│ └── selected_genes_list → Selected genes list
├── mapped_gene_lists/
│ └── selected_genes_list_map → Mapped selected genes list
└── gsea/
├── parameters_log2FC_A_SCI_A_Sham → GSEA parameters run files (one per set run)
└── preranked_gene_lists/ → Generated Preranked Gene lists
├── log2FC_A_SCI_A_Sham.rnk
├── log2FC_A_SCI_A_Sham.rnk
└── log2FC_A_Sham_M_Sham.rnk
# Enrichment Analysis results
/data/
├── gprofiler/
│ └── selected_genes_list/
│ ├── enrichment_fields.tsv → Enrichment results fields provided by gProfiler
│ ├── enrichmed_terms_annotations.tsv → Enriched terms annotations mapping summary
│ └── source/annotations/* → Raw enriched terms annotations sources
├── panther/
│ └── selected_genes_list/
│ ├── enrichment_fields.tsv → Enrichment results fields provided by PANTHER
│ ├── enrichmed_terms_annotations.tsv → Enriched terms annotations mapping summary
│ └── source/annotations/* → Raw enriched terms annotations sources
└── gsea/
└── results/
├── log2FC_A_SCI_A_Sham.combined.GseaPreranked/*
├── log2FC_M_SCI_M_Sham.combined.GseaPreranked/*
└── log2FC_A_Sham_M_Sham.combined.GseaPreranked/
├── enrichment_fields.tsv → Enrichment results fields provided by GSEA
├── enrichmed_terms_annotations.tsv → Enriched terms annotations mapping summary
├── source/annotations/* → Raw enriched terms annotations sources
└── raw_GSEA_output.zip → Raw GSEA output report files