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rmgpanw/gtexr
pkgcheck results - ropensci-software-review

Checks for gtexr (v0.1.0.9000) git hash: 18dc26d7 - :heavy_check_mark: Package is already on CRAN. - :heavy_check_mark: has a codemeta.json file. - :heavy_check_mark: has a contributing file. ...
  • github-actions[bot]
  • 15
  • Opened 
    on Feb 7
  • #14

rmgpanw/gtexr
Release gtexr 0.1.0

First release: - [x] usethis::use_news_md() - [x] usethis::use_cran_comments() - [x] Update (aspirational) install instructions in README - [x] Proofread Title: and Description: - [x] Check ...
  • rmgpanw
  • Opened 
    on Sep 18, 2024
  • #13

rmgpanw/gtexr
Use `get_tissue_site_detail()` instead of `available_tissueSiteDetailIds()`

available_tissueSiteDetailIds() is a not required as the same information (and more) is provided by get_tissue_site_detail() - [x] Remove available_tissueSiteDetailIds.R and test-available_tissueSiteDetailIds.R ...
enhancement
  • rmgpanw
  • Opened 
    on Jun 26, 2024
  • #12

rmgpanw/gtexr
Relay informative errors to app users

For example, supplying . to .featureId in get_genomic_features() produces the following error message: Error: An error has occurred. Check your logs or contact the app author for clarification. - ...
bug
help wanted
  • rmgpanw
  • Opened 
    on Jun 10, 2024
  • #11

rmgpanw/gtexr
Add progress spinner for long running API queries

e.g. for download() - [ ] Use cli package for progress spinner/bar or just a message - [ ] Also add progress bar when usingpurrr::map to process long lists returned from long running API queries
enhancement
  • rmgpanw
  • Opened 
    on May 28, 2024
  • #10

rmgpanw/gtexr
Metadata Endpoints - create R functions

Create R functions for each endpoint listed under Metadata Endpoints. - [x] Get Dataset Info
  • rmgpanw
  • Opened 
    on Apr 14, 2024
  • #9

rmgpanw/gtexr
Histology Endpoint - create R functions

Create R functions for each endpoint listed under Histology Endpoints - [x] Get Image
complete_api_endpoints
  • rmgpanw
  • Opened 
    on Apr 14, 2024
  • #8

rmgpanw/gtexr
Expression Data Endpoints - create R functions

Create R functions for each endpoint listed under Expression Data Endpoints. - [x] Get Expression Pca - [x] Get Gene Expression - [x] Get Median Exon Expression - [x] Get Clustered Median Exon ...
complete_api_endpoints
  • rmgpanw
  • Opened 
    on Apr 14, 2024
  • #7

rmgpanw/gtexr
Datasets Endpoints - create R functions

Create R functions for each endpoint listed under Dataset Endpoints. - [x] Get Annotation - [x] Get Collapsed Gene Model Exon - [x] Get File List - [x] Get Downloads Page Data - [x] Get Full ...
complete_api_endpoints
  • rmgpanw
  • Opened 
    on Apr 14, 2024
  • #6

rmgpanw/gtexr
Improve default arguments for `get_exons()`; add example for

GTEx Portal API documentation states A dataset ID or both GENCODE version and genome build must be provided. I am uncertain how to provide gencodeVersion and genomeBuild, but not datasetId (which has ...
bug
  • rmgpanw
  • 1
  • Opened 
    on Apr 10, 2024
  • #5
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