Additional File 1: Table S1

Table S1 contains the comparison of tools for assisting the interpretation of transcriptome data via functional enrichment analyses.

The explanations for the assessment criteria are provided below.



Here is the key with the different criteria explained

Criterium Description
tool_name Name of the tool/software
link_source Link to the source code of the software
doi_manuscript Link to the manuscript via doi
project_homepage Link to the project homepage (might coincide with source code repository)
available_documentation_demo Levels of documentation available (software docs, vignette, demo website)
input_formats_interoperability Accepted input objects and formats, focused on the interoperability of tools
perform_enrichment_analysis Functionality to perform enrichment analyses in the tool itself
integration_expression_data Functionality to integrate expression data (as effect size with logFC, full usage of expression matrix)
visual_summaries_GOgraphs Functionality to generate visual summaries, including graphs and network on the Gene Ontology terms
interactive_viz_drilldown Features enabling interactive visualizations and results, also for performing drilldown operations for more detail
reproducibility_reports_sessions Functionality to support reproducible analyses (scripts, reports, sessions/bookmarking)
bioconductor_integration Available in Bioconductor/supporting integration with Bioconductor classes
software_language Languages used for the software implementation
software_packaged Availability as software package
software_license Software license (if specified)
usage_modality Software to be run locally or accessible on a server
installation_usability Ease of installation if running locally
misc_info Additional information

Misc

The content of this document has been generated based on the code available at the repository https://github.com/federicomarini/GeneTonic_supplement.

The information in the tables above are extracted from a Google Sheet, available at https://docs.google.com/spreadsheets/d/1EQD8gNk6NID_8CJ-xetQm31XB4eRCXIsvVd4X0oaoPo/edit?usp=sharing.

The last update to the Sheet (and to this document) has been done on 2022-03-01.

The links included in the table have been validated with awesome_bot (https://github.com/dkhamsing/awesome_bot).

Contact info

Is some information not completely correct or up to date?
Do you want to insert an additional tool into the table?

Please contact Federico Marini () with a detailed report or suggest the changes in the Google Sheet.