Skip to content

feature(filter-subnetwork): Add feature to filter the subnetwork from INDRA by query context #84

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
tonywu1999 merged 8 commits into from
Mar 11, 2026
Merged

feature(filter-subnetwork): Add feature to filter the subnetwork from INDRA by query context #84

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
e261ab1
cosine similarity is somewhat promising, considering you can get a ch…
tonywu1999 Nov 6, 2025
320e50c
add vignette for filtering subnetwork by context
tonywu1999 Mar 10, 2026
18dae12
add tags count trick
tonywu1999 Mar 11, 2026
8d48b89
fix bugs
tonywu1999 Mar 11, 2026
b6f513e
address coderabbit comments
tonywu1999 Mar 11, 2026
ca876c4
add basic unit tests
tonywu1999 Mar 11, 2026
30a8d70
finalizing vignettes
tonywu1999 Mar 11, 2026
d4bac72
fix coderabbit comments validation
tonywu1999 Mar 11, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 5 additions & 1 deletion DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,11 @@ Imports:
tidyr,
htmlwidgets,
grDevices,
stats
stats,
text2vec,
stopwords,
xml2,
rentrez
Suggests:
data.table,
BiocStyle,
Expand Down
15 changes: 15 additions & 0 deletions NAMESPACE
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ export(annotateProteinInfoFromIndra)
export(cytoscapeNetwork)
export(cytoscapeNetworkOutput)
export(exportNetworkToHTML)
export(filterSubnetworkByContext)
export(getSubnetworkFromIndra)
export(previewNetworkInBrowser)
export(renderCytoscapeNetwork)
Expand All @@ -16,13 +17,27 @@ importFrom(httr,GET)
importFrom(httr,POST)
importFrom(httr,add_headers)
importFrom(httr,content)
importFrom(httr,content_type_json)
importFrom(httr,status_code)
importFrom(jsonlite,fromJSON)
importFrom(jsonlite,toJSON)
importFrom(r2r,hashmap)
importFrom(r2r,keys)
importFrom(r2r,query)
importFrom(rentrez,entrez_fetch)
importFrom(stats,cor)
importFrom(stats,setNames)
importFrom(stopwords,stopwords)
importFrom(text2vec,TfIdf)
importFrom(text2vec,create_dtm)
importFrom(text2vec,create_vocabulary)
importFrom(text2vec,fit_transform)
importFrom(text2vec,itoken)
importFrom(text2vec,prune_vocabulary)
importFrom(text2vec,vocab_vectorizer)
importFrom(text2vec,word_tokenizer)
importFrom(tidyr,pivot_wider)
importFrom(utils,browseURL)
importFrom(xml2,read_xml)
importFrom(xml2,xml_find_all)
importFrom(xml2,xml_text)
Loading
Loading