Changelog

EnrichGT 0.2.9

Package major update

• infering_regulator_act() to infer pathway or transcript factors activity from EnrichGT meta-gene modules.

• This will be the end of new functions of EnrichGT package.

EnrichGT 0.2.8.x

Package major update

• EnrichGT() now supports changing hclust() methods, like using ward.D, ward.D2, average …

• EnrichGT_obj now contains a slot clustering_tree containg the cluster tree hclust object, for further analysing and drawing figures.

• EnrichGT_obj now contains raw table. (0.2.8.5)

Others

• Add benchmark markdown file

• Refine the help pages

EnrichGT 0.2.7

Package major update

• Add CompareGT() function (beta)

EnrichGT 0.2.5

Package major update

• Bug fix

• EnrichGT() supports a list containing multiple source enrichment results (e.g., GO and KEGG enrichment for a same DEG list), and fusing them. User can gain Metascape like multi-DB enrichment result by using the fusing function (See Articles).

EnrichGT 0.2.0

Package major update

• Bug fix in generating results.

• Add EnrichGT_obj S4 object. It not only returns gt HTML tables, users can extract enriched tables, meta-gene modules, pathway modules in it.

Others

• Split main.R to multiple files, for better managing of codes.

• Add package vignettes.

EnrichGT 0.1.7

Package major update

• add doGO(), doKEGG(), doRA() wrapper for ORA enrichment.

• add BuildMultigroupDEGlist() and Ranked.GS() for simplifying procedure of multi-group enrichment and GSEA.

EnrichGT 0.1.2

Package major update

• Support GSEA results.

• Give up ggplot2 figures in gt object for speed up. Though the result is much ugly than before :)

• Intelligent sensing the cluster numbers.

• Provide self-check of column names, if setReadable() before, etc.

Others

• Auto check package dependencies when start-up.

EnrichGT 0.1.0

• Initial codes for generating gt objects for ORA objects.

• Initial codes for enrichment, use text2vec package to parse core enriched genes.