genefeast 0.0.15

Gene-centric functional enrichment analysis summarisation tool

GeneFEAST

GeneFEAST, implemented in Python, is a gene-centric functional enrichment analysis summarisation and visualisation tool that can be applied to large functional enrichment analysis (FEA) results arising from any upstream FEA pipeline. It produces a systematic, navigable HTML report, making it easy to identify sets of genes putatively driving multiple enrichments and to explore gene-level quantitative data first used to identify input genes. Further, GeneFEAST can compare FEA results from multiple studies, making it possible to, for example, highlight patterns of gene expression amongst genes commonly differentially expressed in two sets of conditions, and giving rise to shared enrichments under those conditions. GeneFEAST offers a novel, effective way to address the complexities of linking up many, overlapping FEA results to their underlying genes and data; advancing gene-centric hypotheses, and providing pivotal information for downstream validation experiments.

Installation

We strongly recommend installing GeneFEAST in a virtual environment because the library has several requirements:

• python == 3.7
• matplotlib == 3.3.3
• numpy == 1.17.2
• pandas == 0.25.2
• upsetplot == 0.4.1
• goatools == 1.0.14
• scipy == 1.3.2
• networkx == 2.5
• lxml == 4.4.1
• beautifulsoup4 == 4.8.0
• pillow == 6.2.0
• PyYAML == 5.1.2

Please follow the instructions at the top of this guide to create and activate a virtual environment. Please only follow the instructions to the end of section Activating a virtual environment and then come back here.

Once you have created and activated your virtual environment, you can install the library using pip:

$ pip install genefeast

Usage

To run GeneFEAST you will need:

• A comma-delimited file containing the results of a functional enrichment analysis (FEA). GeneFEAST expects a file containing the following ten columns, in this order:

  • Type (required)
  • ID (required)
  • Description (required)
  • GeneRatio (only required when dot plots are switched on)
  • BgRatio (only required when dot plots are switched on)
  • pvalue (optional; field can be empty)
  • p.adjust (required)
  • qvalue (optional; field can be empty)
  • geneID (required. This should be a "/" delimited list of gene IDs. The gene IDs must match those used in the genes of interest file (see next))
  • count (only required when dot plots are switched on)

• A file containing a list of genes of interest, one per line, each with their corresponding quantitative data (eg log2 fold change from an RNASeq analyses). Please note:

  • Genes of intersest must be listed using IDs that match those used in the FEA results file.
  • There can be other columns in the file - these will be ignored.
  • You will use the config file (see below) to tell GeneFEAST which column contains gene IDs, and which column contains quantitative data.
  • If you do not have quantitative data, you can just provide a dummy column with the same numerical value entered for each gene.