v3.0

New features

• Added new metrics:
  • transcription factor cluster specificity
  • median coexpression score of transcription factors and their target genes
• Updated centrality metrics:
  • for regulons where closeness and betweenness are not defined at the cluster level (e.g., when the TF doesn’t have incoming edges), the closeness and betweenness values are now computed based on the original network after motif mapping filtering
  • per-cluster closeness and betweenness are always assigned better ranks compared to the original closeness and betweenness values
• Improved TF prioritization in the Reference procedure (used when a list of (GO) terms of interest is specified by the user)
• New parameter: users can now specify a custom background for the enrichment analysis (when not specified, the background defaults to the list of genes that are present in the expression matrix)
• Expanded input options: terms of interest can now also be specified as ontology terms (e.g., GO:0009819), in addition to (or instead of) plain English words (e.g., drought)

Improvements and bug fixes

• Input file verification is now more efficient and thorough
• Additional information is included in the log file for improved transparency
• Minor improvements and bug fixes

Full Changelog: v2.2...v3.0

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