Changelog

Source: NEWS.md

icWGCNA 0.4.0

New Features

• display_top_genes() to identify top gene and/or values of communities

Other Changes

• Renamed gene_mapping() to expression_compression(), and parameter mapping_file to mapping_df. gene_mapping() name kept for backwards compatibility.

icWGCNA 0.3.0

New Features

• map_eigengenes_on_seurat() to map eigengenes on a Seurat Object

icWGCNA 0.2.5

New Features

• find_unique_top_genes() to identify top gene of communities that are unique (only belong to one community)

Other Changes

• Removed uncorrected_community_signature output from icwgcna()
  • Now users should run compute_eigengene_matrix() after icwgcna()if uncorrected community signatures are needed.

icWGCNA 0.2.4

• Fixed bug in compute_eigengene_matrix() when all genes are above cutoff

icWGCNA 0.2.3

New Features

expression_compression() function for converting between gene types (i.e. ENTREZ to Hugo), which many options for compression of duplicate rows.

Other Changes

• Minor bug fixes
• Switching to fastcluster::hclust() from stats pacakge (#16)

icWGCNA 0.2.2

• Bug fixes and internal function improvements
• Add p value output for compute_MSigDB_enrichment()
• Add full_metaGenes and full_eigenGenes output for icwgcna()

icWGCNA 0.2.1

Bug fixes and checking for PC1 > 35% in input expression

icWGCNA returns uncorrected_community_signature instead of full_community_membership and full_community_signature

icWGCNA 0.2.0

New Features

Enrichments Functions

• compute_MSigDB_enrichment() (with parallel and distributed processing)
• compute_xCell_enrichment()

UMAP Plotting

• make_network_umap()

icWGCNA 0.1.1

Released on public Github.

icWGCNA 0.1.0

Initial release to be shared publicly

Bug Fixes

Better panglaoDB variable name matches and error catching (#18)

Downstream functions improvement and error catching

icWGCNA 0.0.0.9002

Bug Fixes

Fixed error when genes have 0 standard deviation (#16)

icWGCNA 0.0.0.9001

First Version