InterMineR
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intermine
R package for InterMine
Running the example in the tutorial (https://rdrr.io/bioc/InterMineR/f/vignettes/Enrichment_Analysis_and_Visualization.Rmd) does not work any more after upgrading bioconductor to 3.13. It throws out the following error: ``` Error in (function (classes, fdef, mtable)...
The (HTTP) 400 Bad Request response status code is returned.
Citation is not working. Info on Bioconductor page > Citation (from within R, enter citation("InterMineR")): Important note to the maintainer of the InterMineR package: An error occured while trying to...
doEnrichment functions returns "HTTP 414" error when number of gene is 300, there are no problem when this number is less than 100.
Currently you can only query production InterMines. There is a use case for being able to query dev mines, e.g FlyMine beta.
Unless I've missed it, there doesn't appear to be any inbuilt way to handles lists, e.g. - fetch a list by name - save a list - Perform list ops...
One another idea that I had, a feature related to not finding hits, that could be useful: in the InterMineR library, the function runQuery() returns only the matches. However the...
`ONE OF` constraints aren't handled correctly by InterMineR and convert to invalid query XML. ```r pancreasConstraint1 = setConstraints( paths = c("Gene", "Gene.proteinAtlasExpression.level", "Gene.proteinAtlasExpression.tissue.name"), operators = c("IN", "ONE OF", "="), values...
Hello, It seems that the population argument in the doEnrichment function only accepts names of public lists at the moment (giving it a private list with API token/key from MyMine...
https://bioconductor.org/packages/release/bioc/vignettes/InterMineR/inst/doc/Enrichment_Analysis_and_Visualization.html#piechart-and-barplot-graphs Pies and bar charts are pretty, but given the fact that a smaller P value is better, it takes some figuring out to understand what's going on - the...