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phenoscape
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rphenoscape
R package to make phenotypic traits from the Phenoscape Knowledgebase available from within R.
https://rphenoscape.phenoscape.org/
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Fixes use of environment for KB API endpoint
#188
hlapp
closed
3 years ago
0
Fixes RNeXML links in documentation
#187
johnbradley
closed
3 years ago
0
Fix RNeXML links in documentation
#186
johnbradley
closed
3 years ago
7
Removes pk_ prefix from term.R functions
#185
johnbradley
closed
3 years ago
0
Removes pk prefix from pk_is_descendant/pk_is_ancestor
#184
johnbradley
closed
3 years ago
0
Remove limit work around
#183
johnbradley
closed
3 years ago
5
Runs tests against phenoscape dev server
#182
johnbradley
closed
3 years ago
0
Automate testing kb.phenoscape API dev endpoint
#181
johnbradley
closed
3 years ago
1
Improve parameter handling in get_ontotrace_data
#180
johnbradley
closed
3 years ago
15
Replace for loops with apply
#179
johnbradley
closed
3 years ago
3
Improve descendant/ancestor functions
#178
johnbradley
closed
3 years ago
1
Improve term detail functions
#177
johnbradley
closed
3 years ago
1
Improves names of pk_get_ontotrace_xml and pk_get_study_xml functions
#176
johnbradley
closed
3 years ago
9
Regenerates term_classification docs
#175
johnbradley
closed
3 years ago
0
Regenerate documentation for term_classification
#174
johnbradley
closed
3 years ago
1
Consistently use mssg instead of message
#173
johnbradley
closed
3 years ago
2
Evaluate suitability of NeXML data extracting functions
#172
johnbradley
closed
3 years ago
7
Removes hard coded phenoscape api URLs
#171
johnbradley
closed
3 years ago
0
Fixes filename for term_classification
#170
hlapp
closed
3 years ago
0
Regenerate Rd files for baseline-v0.3.0
#169
johnbradley
closed
3 years ago
1
Update Rd files for baseline-v0.3.0 branch
#168
johnbradley
closed
3 years ago
1
Replace calls to pk_GET with get_json_data
#167
johnbradley
closed
3 years ago
1
Use pkb_api instead of hard coded phenoscape API URLs
#166
johnbradley
closed
3 years ago
1
Updates github action tests to run every Thursday
#165
johnbradley
closed
3 years ago
1
Run tests on a weekly basis
#164
johnbradley
closed
3 years ago
0
Replaces pk_*_class with term_classification
#163
johnbradley
closed
3 years ago
12
Filters out label-less terms from flagged ontologies
#162
hlapp
closed
3 years ago
1
Some terms expected to receive a label do not
#161
hlapp
closed
3 years ago
0
Fixes handling of term freqs that are missing or zero
#160
hlapp
closed
3 years ago
1
Fixes expected number of exact matches
#159
hlapp
closed
3 years ago
0
Restores the earlier ProgressReporter type of test output
#158
hlapp
closed
3 years ago
1
Handles HTTP 404 returned for no matches
#157
hlapp
closed
3 years ago
0
Fixes HTTP error reporting
#156
hlapp
closed
3 years ago
0
Update README badge for github actions
#155
johnbradley
closed
3 years ago
0
Replace Travis-CI based badge in README with one based on GitHub Actions status
#154
hlapp
closed
3 years ago
0
Semantic similarity tests fail
#153
hlapp
closed
3 years ago
3
Taxon IRI retrieval fails
#152
hlapp
closed
3 years ago
1
Taxon details test fails
#151
hlapp
closed
3 years ago
2
usethis::use_github_action("check-standard")
#150
johnbradley
closed
3 years ago
4
Ensure proper working CI test, including on 0.2.x release series
#149
hlapp
closed
3 years ago
1
pk_get_ontotrace warning message
#148
wdahdul
closed
3 years ago
2
Provides an in-memory cache initializable from file
#147
hlapp
opened
4 years ago
0
Introduces parameter to allow forcing a GET request
#146
hlapp
closed
4 years ago
0
as.phenotype() fails for very long phenotype URIs
#145
hlapp
closed
4 years ago
0
Implements profile similarity
#144
hlapp
closed
4 years ago
0
Improves recovery of labels for pregenerated post-comps
#143
hlapp
closed
4 years ago
0
Adds Resnik (MICA) similarity
#142
hlapp
closed
4 years ago
0
Improves term frequency calculation for taxon annotations
#141
hlapp
closed
4 years ago
0
Improves success rate of auto-determining term type
#140
hlapp
closed
4 years ago
0
Complete tests of term_freqs() for genes corpus
#139
hlapp
opened
4 years ago
0
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