GEOquery
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seandavi
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
**Describe the bug** Cannot open dataset as described in first lines of R script [here](https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE425) **To Reproduce** Steps to reproduce the behavior including code example: ```r library(GEOquery) gset
getGEO
When I use the function 'getGEO',I get the errow below: Error in app$vspace(new_style$`margin-top` %||% 0) : attempt to apply non-function
Unfortunately `base` `R`'s functions have some imperfections; use `fs` instead. I was reading `getGEOSuppFiles` and found use of `file.path` across the whole package. ```r url
?`GEOData-accessors` shows > The main documentation is in the Class documentation Going to GEOData-class has only one sentence > A virtual class for holding GEO samples, platforms, and datasets and...
Came across another problematic GEO dataset I thought I would report ([GSE136400](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE136400)): **Code to reproduce**: ```r library(GEOquery) getGEO('GSE136400') ``` **Output / Error message**: ``` Found 1 file(s) GSE136400_series_matrix.txt.gz Using locally...
Is it possible to change the default amount for soft files to "data" for GPL files? The files would be smaller, because there will be no sample listing. In my...
Hi, when converting GSE to an ExpressionSet, you suggest in your help package to : `probesets
I can get the usual information from the below GSE but I can not find a way to read the `series_table` where the authors keep track of each single cell...
The Description part is about GEO SOFT format files. However, these kinds of files are not download by default, unless `GSEmatrix` is changed to FALSE. The Details section also seems...