bigslu/searchways

SEARchways

searchways's Issues

Multiple subcategories

Add functionality for BIGsea and BIGprofiler to run multiple subcategories at once,

Harmonize column names

Describe the solution you'd like
Make the column names consistent in all enrichment and gsea functions. Make sure to update BIGpicture functions as necessary.

BIGsea multi and label

Is your feature request related to a problem? Please describe.
Update BIGsea to support simple (current), multi (now recommended by fgsea), and label (recommended by Broad when you have sufficient samples).

Describe the solution you'd like
Add parameter to BIGsea with options c("simple","multi","label")

See https://rdrr.io/github/ctlab/fgsea/src/R/fgsea.R

BIGprofiler not robust to no genes found in gene sets

Describe the bug
When none of the query genes are in the gene data base, BIGprofiler fails and breaks Rmd and loops

Expected behavior
Output a warning that no genes were mapped and return a NULL result

GO ID

Is your feature request related to a problem? Please describe.
GO gene set names do not match other databases such as GOdb

Describe the solution you'd like
Include GO ID (named gs_exact_name) in the results

rrvgo like grouping of gene sets

Describe the solution you'd like
Add functions to calculate semantic similarity between gene sets and plot in MDS, similar to rrvgo for C5 GO terms

adjust minGSSize and maxGSSize

Is your feature request related to a problem? Please describe.
The custom databases I'm using have gene set sizes outside of the default range for clusterProfiler::enricher (10 to 500)

Describe the solution you'd like
Add optional parameters to adjust acceptable gene set sizes

BIGprofiler categories

Describe the bug
BIGprofilter( ) does not work for the newer MSigDB categories (like C8, M8)