Table S1 contains the comparison of tools for Differential Expression analysis.
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 |
| heatmaps_clustering_genes | Can the software generate heatmaps or clustering of genes? |
| pca_mds | Can the software perform PCA or MDS? |
| volcano_maplot | Can the software generate summary plots like MA plots or volcano plots? |
| singlegene_plot | Can the software create single gene plots? |
| differential_expression | Can the software perform Differential Expression analysis? |
| pathway_analysis | Can the software perform some functional enrichment analysis? |
| id_conversion | Can the software handle the conversion of different identifiers? |
| complex_models | Can the software handle complex models in Differential Expression analysis? |
| external_apis | Does the software link/refer/integrate automatically some external sources of information (e.g. for cross-referencing) |
| input_formats | Can the software handle different types of input? |
| feat_sample_filtering | Can the software perform filtering at the feature and sample level? |
| tx_level_analysis | Can the software perform transcript level analysis? |
| report_generation | Does the software generate some report as product of the analysis? |
| state_saving | Can the software save its state? |
| support_bioc_formats | Does the software handle standard Bioconductor classes and formats? |
| software_packaged | How the software is available/distributed |
| bioconductor_pkg | Is the software available on Bioconductor? |
| deploy_info | Is there sufficient info on how to deploy this tool (in a server-like mode)? |
| demo_available | Is a demo instance available? |
| batch_effect_correction | Can the software perform some type of batch correction on the data? |
| software_license | License (if specified) |
| software_language | Languages used for the implementation |
| misc_info | Some additional comments |
The content of this document has been generated based on the code available at the repository https://github.com/federicomarini/ideal_supplement.
The information in the tables above are extracted from a Google Sheet, available at https://docs.google.com/spreadsheets/d/167XV0w18P0FSld1dt6owN4C2Esxl5FU2QTo4D-wclz0/edit?usp=sharing.
The last update to the Sheet (and to this document) has been done on 2020-01-09.
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.