karissawhiting/cbioportalR issues and pull requests

#76 - Unable to connect to the internal MSK API

Issue - State: open - Opened by jgarces02 5 days ago - 2 comments

#75 - Download GENIE BPC CRC v2.0-public

Issue - State: closed - Opened by drhmoosavi 2 months ago - 1 comment

#74 - Could not connect to Genie db

Issue - State: closed - Opened by Almogkm 7 months ago - 1 comment

#73 - get_study_info() refers to incorrect function

Issue - State: closed - Opened by clarrity 8 months ago - 2 comments

#72 - available_studies()

Issue - State: closed - Opened by kmezhoud 8 months ago - 1 comment

#71 - How to get mRNA expression profiles

Issue - State: open - Opened by ypradat 8 months ago - 2 comments
Labels: enhancement

#70 - available_studies() API request failed 404

Issue - State: closed - Opened by ypradat 8 months ago - 2 comments

#69 - Release cbioportalR 1.1.0

Issue - State: closed - Opened by karissawhiting 12 months ago

#68 - cbioportalR v1.1.0 CRAN Submission

Issue - State: closed - Opened by karissawhiting 12 months ago

#65 - Get study id for samples

Pull Request - State: open - Opened by karissawhiting over 1 year ago

#64 - Add segmentation pull

Pull Request - State: open - Opened by karissawhiting over 1 year ago

#63 - purr::list_flatten bug

Issue - State: closed - Opened by karissawhiting over 1 year ago

#62 - Allow namespace cols

Pull Request - State: closed - Opened by karissawhiting over 1 year ago - 5 comments

#61 - added arguments to extra-packages

Pull Request - State: closed - Opened by michaelcurry1123 almost 2 years ago

#60 - update r-cmd to v2

Pull Request - State: closed - Opened by michaelcurry1123 almost 2 years ago

#59 - update pkgdown to v2

Pull Request - State: closed - Opened by michaelcurry1123 almost 2 years ago

#58 - update to version 2 for test-coverage

Pull Request - State: closed - Opened by michaelcurry1123 almost 2 years ago

#57 - Warning message when setting cbioportal database

Issue - State: closed - Opened by edrill almost 2 years ago - 1 comment

#56 - get_clinical_by_study() returns file with no sample IDs.

Issue - State: closed - Opened by edrill almost 2 years ago - 1 comment

#55 - fix cli errors from newest version of cli package

Pull Request - State: closed - Opened by karissawhiting almost 2 years ago

#53 - Request for feature - sample_ids per study per molecule-profile

Issue - State: closed - Opened by morriso1 about 2 years ago - 1 comment

#52 - Add segmentation retrieval endpoint

Issue - State: open - Opened by karissawhiting about 2 years ago

#51 - V1.0.1 feedback

Pull Request - State: closed - Opened by karissawhiting about 2 years ago

#50 - Feedback before submission of v1.0.1

Issue - State: closed - Opened by karissawhiting about 2 years ago - 9 comments

#49 - Update all examples and tests to skip CRAN

Pull Request - State: closed - Opened by karissawhiting about 2 years ago

#48 - Get example cBioPortal study setup to use for tests and examples

Issue - State: open - Opened by karissawhiting about 2 years ago

#46 - Post CRAN Release, Set up Development Version

Pull Request - State: closed - Opened by karissawhiting about 2 years ago

#45 - cbioportalR v1.0.0 CRAN Submission

Issue - State: closed - Opened by karissawhiting about 2 years ago - 1 comment

#44 - I noticed pipes and pulls are frequently used on the package website in the Examples, but the dplyr package was not mentioned on this page (it is mentioned on the vignette page)– really not a big deal, but for brand new R users it may be helpful to mention that pipes and pulls require dplyr to be loaded, or simply add a line with “library(dplyr)” at the beginning of Example :)

Issue - State: closed - Opened by karissawhiting about 2 years ago

#43 - Review for CRAN release (v.1.0.0)

Issue - State: closed - Opened by karomanchuk about 2 years ago - 1 comment

#42 - Prep for v1.0.0 Cran Submission

Pull Request - State: closed - Opened by karissawhiting over 2 years ago - 1 comment

#41 - Allow less strict df names

Pull Request - State: closed - Opened by karissawhiting over 2 years ago - 1 comment

#40 - Allow users to pass a panel ID sample ID pulls

Pull Request - State: closed - Opened by karissawhiting over 2 years ago

#39 - Get study ID corresponding to a sample ID

Issue - State: open - Opened by karissawhiting over 2 years ago

#38 - Pull virtual study details by session info

Issue - State: open - Opened by karissawhiting over 2 years ago

#37 - Pull by sample ID without specifying genes

Pull Request - State: closed - Opened by karissawhiting over 2 years ago

#36 - update get_xx_by_sample to accept hugo symbol

Pull Request - State: closed - Opened by jalavery over 2 years ago - 1 comment

#35 - Update overview-of-workflow.Rmd

Pull Request - State: closed - Opened by jalavery over 2 years ago

#34 - update clinical by study to include patient and sample

Pull Request - State: closed - Opened by karissawhiting over 2 years ago - 1 comment

#33 - Allow user to pass hugo_symbol to `get_genomics_by_sample()` set of functions

Issue - State: closed - Opened by karissawhiting over 2 years ago

#32 - update readme

Pull Request - State: closed - Opened by karissawhiting over 2 years ago

#31 - add patient level functions

Pull Request - State: closed - Opened by karissawhiting over 2 years ago

#30 - Add hugo by study

Pull Request - State: closed - Opened by karissawhiting over 2 years ago - 2 comments

#29 - get pr template

Pull Request - State: closed - Opened by karissawhiting over 2 years ago

#28 - Add hugo symbol

Pull Request - State: closed - Opened by karissawhiting over 2 years ago

#27 - Update hex, code of conduct and contributing guide

Pull Request - State: closed - Opened by karissawhiting over 2 years ago

#26 - Potentially Update cli_abort() with rlang::abort()

Issue - State: closed - Opened by karissawhiting over 2 years ago - 1 comment

#25 - Update Hex Sticker to New Version

Issue - State: closed - Opened by karissawhiting over 2 years ago - 1 comment

#24 - Update README to Also Suggest Using {keyring} to Hold cBioPortal Authentication Info

Issue - State: open - Opened by karissawhiting over 2 years ago - 2 comments

#23 - Allow all `*by_sample()` Functions to Accept Sample-study Pairs df as Arguments

Issue - State: closed - Opened by karissawhiting over 2 years ago - 1 comment

#22 - Add Contributing Guide and Code of Conduct

Issue - State: closed - Opened by karissawhiting over 2 years ago - 1 comment

#21 - Fix Diagram on gh-pages of README

Issue - State: closed - Opened by karissawhiting over 2 years ago

#20 - Create PR Template

Issue - State: closed - Opened by karissawhiting over 2 years ago

#19 - add hex sticker, update function names, add genes arg, and small fixes

Pull Request - State: closed - Opened by karissawhiting over 2 years ago

#18 - Change 'Master' Branch to 'Main'

Issue - State: closed - Opened by karissawhiting over 2 years ago

#17 - Allow passing of `df_pairs` to `get_clinical_by_sample()`

Issue - State: closed - Opened by karissawhiting over 2 years ago - 1 comment
Labels: priority

#16 - Allow `sample_study_pairs` Argument in `get_*_by_sample()` To Accept Raw Column Names (e.g. sampleId)

Issue - State: closed - Opened by karissawhiting over 2 years ago

#15 - Add Gene Panel As Argument to Get Genomics Functions

Issue - State: closed - Opened by karissawhiting over 2 years ago

#14 - Add Hugo Symbol to Genomic Results

Issue - State: closed - Opened by karissawhiting over 2 years ago - 1 comment
Labels: priority

#13 - badge fix

Pull Request - State: closed - Opened by karissawhiting over 2 years ago

#12 - Create internal-structure vignette

Pull Request - State: closed - Opened by karissawhiting over 2 years ago

#11 - Migrate all post release v0.1.0. changes to the master branch

Pull Request - State: closed - Opened by karissawhiting over 2 years ago

#7 - Bug in fusion data retrieval with get_genetics()

Issue - State: closed - Opened by edrill almost 3 years ago - 1 comment

#6 - test CDKN2A subtypes with API

Issue - State: closed - Opened by karissawhiting over 3 years ago - 1 comment

#5 - Test Package Functions with GENIE Data

Issue - State: closed - Opened by karissawhiting over 3 years ago - 8 comments
Labels: help wanted

#4 - Clinical data that is sample level versus patient level

Issue - State: closed - Opened by karissawhiting over 3 years ago
Labels: priority

#3 - Fix error message when no study_id provided but no non-IMPACT IDs passed

Issue - State: closed - Opened by karissawhiting over 3 years ago

#2 - Test with TCGA data

Issue - State: closed - Opened by karissawhiting over 3 years ago

#1 - Troubleshoot get_segments and add to get_genetics()

Issue - State: closed - Opened by karissawhiting over 3 years ago

GitHub / karissawhiting/cbioportalR issues and pull requests