Supplementary Information for the GeneTonic package
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.
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 |
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).
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 (marinif@uni-mainz.de) with a detailed report or suggest the changes in the Google Sheet.