Sehyun Oh
Update the following URL to point to the GitHub repository of the package you wish to submit to _Bioconductor_ - Repository: https://github.com/shbrief/AnVILWorkflow Confirm the following by editing each check box...
**Background**: Though many omics data repositories host large volumes of datasets from diverse studies, cross-study analysis within these repositories is still somewhat limited due to the heterogeneity in their metadata...
Hi! I have an issue with the extract function on EFO. Here is the script I used: ``` wget http://www.ebi.ac.uk/efo/efo.obo robot extract --method MIREOT \ --input efo.obo \ --branch-from-term "EFO:0000408"...
The publication year in the study name seems wrong for these: PMID 26408641 (published in 2017) - the current study_name is YuJ_2015 PMID 30936548 (published in 2019) - the current...
9e1afa1 If `get_terminal_nodes` is applied after `relativeAb`, the 'non-relative abundance input' warning is triggered. Add this to the documentation.
Rewrite the apply-within-apply part? https://github.com/waldronlab/lefser/blob/b059a6213aed225116e1b62e155280f7d8de60bb/R/lefser.R#L24-L32
Additional visualization options - [ ] Cladogram - [x] Abundance plot (Histogram)
Hi! I'm getting the below error for my query: ``` > cbio_api study samples cBioPortalData( + api = cbio_api, + by = "hugoGeneSymbol", + studyId = study, + sampleIds =...
The error we found should be a fixable error in their relative abundance calculation. Essentially, in their code (and example analysis provided in the manuscript) they take in reads summed...
The `lefserPlotClad` function should perform a sanity check of whether the input has `rowData` properly populated with taxonomy.