[x] Vignette needs an explanation of the connection between get_dataset_differential_expression_analyses and get_differential_expression_values
[x] Output definitions for all functions
[x] Don't forget to remove differentially expressed gene counts if they aren't fixed by release
[x] gemma.R main doc page "Most users will want to start with the high-level functions getDataset, getDatasetDE and getPlatformAnnotations. Additional lower-level methods are available that directly map to the Gemma RESTful API methods." -> revise to use new method names; can these be links to the relevant pages? What about mentioning the search function?
[x] same page: clarify that this is transcriptome data only. The current opening paragraph is more vague than it needs to be.
[x] search_datasets: I'm not sure why the docs so prominently mention taxa. The function should work without consideration of taxon. "Retrieve datasets within a given taxa associated to an annotation tags search" is pretty confusing
[x] get_gene_go_terms: GO terms were updated in June but how do we keep this text up to date? The docs should make it clear that the GO terms are coming from NCBI and are updated periodically. (exposing the update date via the API is on the to-do-list)
oganm
commented
2 years ago
get_dataset_differential_expression_analysesandget_differential_expression_values