TRIAGE v1.1.5

Release Notes

1. Introduction of the 'compareGO' function:

We have added the 'compareGO' function to streamline the visualization of Gene Ontology (GO) enrichment analysis. This function facilitates an efficient comparison of enriched GO terms across specified groups of genes.

2. Enhanced TRIAGEgene functionality:

We have introduced the 'pvalue' parameter in the TRIAGEgene function. This parameter calculates P-values using a rank-based Z-score method, allowing for a statistical evaluation of the regulatory potential of genes.

Coupled with the 'pvalue' parameter, we have also added 'min_comparable_genes' and 'percentile' parameters:
'min_comparable_genes': This parameter specifies the minimum number of comparable genes to use for P-value calculation.
'percentile': This parameter represents the proportion of input genes to be used as comparable genes with similar gene expression values for P-value calculation.

TRIAGE v1.1.4

Release Notes

1. Added the 'topGene' function to extract genes with highest DS values based on the TRIAGEgene output.
2. Revised the 'id' parameter for the 'plotGO' function, allowing users to customize a list of ids for visulization.

TRIAGE v1.1.3

Release Notes

1. Added the 'bw' parameter for TRIAGEcluster, allowing users to customize a list of bandwidths for KDE plots.
2. Revised the parameter description for TRIAGEparser to clarify the usage of 'number_of_gene' based on the input type.
3. Revised the parameter description for plotGO to clarify the usage of 'top_terms'.
4. Added the 'fdr' parameter for plotGO, allowing users to customize the FDR threshold for the heatmap visualisation of the TRIAGEparser results.
5. Added the 'getClusterGenes' function to extract genes assigned to a specific cluster based on the highest probability from the TRIAGEparser output, facilitating downstream analyses for individual gene clusters.
6. Added the 'prefix' parameter for the 'byPeak' function to define the column names in the output file.

TRIAGE v1.1.2

Release Notes

1. Updated parameters ("cell_column", "peak_column") for the 'byPeak' function.
2. Added the seed option for TRIAGEcluster to ensure reproducibility of random processes.
3. Fixed a bug in TRIAGEcluster that caused the error: "Error in value[[3L]]". This update also suppresses Pandas 'SettingWithCopyWarning' messages, ensuring smoother operation and a better user experience.
4. Added size parameters (width and height) for the 'plotGO' function, allowing users to customize the size of the heatmap PDF file.
5. Adjusted the row fontsize when the GO label is very long in the 'plotGO' function, improving readability.

v1.1.1

TRIAGE v1.1.1

This new release (TRIAGE v1.1.1) addresses a minor bug fix in the roadmap and epimap gene lists.

v1.1.0

The TRIAGE R package has been updated to version 1.1.0. This update includes bug fixes and changes the package name from "Triage" to "TRIAGE". Users should now use library(TRIAGE) instead of library(Triage) to access the package.