v2.2

New features

• A list of transcription factors was added for all the supported species
• The user can now specify the output directory by modifying the outputDir parameter
• After a successful run, a log file is generated in the output directory, summarising statistics on the input dataset(s), information on the provided input files and parameters, as well as intermediary results in the workflow
• Gene aliases file made optional
• Output figures are also generated in PNG format
• Ranked regulons file is also generated in TSV format

Improvements and bug fixes

• Arabidopsis GO files regenerated to include high-throughput evidence codes
• GO files regenerated to exclude duplicated entries
• Improved verification of the input files and parameters
• Improved the layout of the config file + added more comments
• Improved the layout of the output figures
• Number of CPUs specified for the GRNBoost2 procedure is now correctly taken into account
• Corrected enrichment algorithm that was not always using the correct background size
• Corrected file extensions for input and output tab delimited files
• Where possible, TF information is extracted from TF list file instead of TF2fam2mot file, removing the need for this file when running MINI-EX without the motif enrichment step
• Minor bug fixes

Full Changelog: v2.1...v2.2

v2.1

New features

• Added support for maize AGPv5

Improvements

• Regenerated GO files to include non-experimental evidence codes
• Enhanced handling of executors, allowing to easily switch between different job schedulers
• Improved display of gene aliases on figures
• Error corrections in gene alias files
• Updated structure of data folders
• Minor bug fixes

Full Changelog: v2.0...v2.1

v2.0

New features

• Added support for Solanum lycopersicum (tomato) (see folder data_sly).
• Added support to omit the motif enrichment analysis. In this mode, all possible species are supported, but note that the resulting networks are more prone to false positives.
• Added a new output format: edge table with regulon rank and edge weights.
• Added regulator heatmap as additional output figure (example).
• Enrichment background is now filtered for expressed genes, usually leading to an increased number of predicted regulons.
• When computing enrichment: minimum number of hits is set to 2 to relax FDR statistics.
• Updated gene GO annotation for Arabidopsis.
• Added gene alias file for Zea mays.
• Added input file validation step.
• Dataset statistics are printed after the input validation step.

Documentation

• Added the pipeline schema with detailed explanations to the README.
• Added constraints for the input files in Prepare your files.
• Added an example of the expression matrix generation from a Seurat object in Prepare your files.
• Added the FAQ.

Full Changelog: v1.0...v2.0

v1.0 - Initial release

Initial release