User: l.nilse

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l.nilse0
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Posts by l.nilse

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Comment: C: Uniprot.ws getting Function [CC]
... Great. Thanks for the fix, James. We will test and then close the GitHub issue. ...
written 20 months ago by l.nilse0
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Comment: C: Uniprot.ws getting Function [CC]
... Thanks, James. - I filed a features request. https://github.com/Bioconductor/UniProt.ws/issues/1 ...
written 20 months ago by l.nilse0
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Comment: C: Uniprot.ws getting Function [CC]
... See column Function [CC] here. https://www.uniprot.org/help/uniprotkb_column_names ...
written 20 months ago by l.nilse0
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UniProt.ws - single database for two species
... UniProt.ws library is a great tool which we are using extensively. With db <- UniProt.ws(taxId=9606) I can read the database for one specific species. How can I generate a database for two species db <- UniProt.ws(taxId=c(9606,10090)) or how can I combine two databases to a single one? Tha ...
uniprot.ws uniprot written 2.1 years ago by l.nilse0 • updated 2.1 years ago by James W. MacDonald52k
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Comment: C: UniProt.ws report 1:many mappings in a single row
... .                    . ...
written 3.0 years ago by l.nilse0
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Answer: A: UniProt.ws report 1:many mappings in a single row
... Here a possible solution complete with an example. Note that there are duplicate entries in the keys and multiple KEGG results. library(UniProt.ws) species <- 9606 # homo sapiens up <- UniProt.ws(taxId=species) UniqueSpaceSeparated <- function(x) { u <- unique(x) r <- paste ...
written 3.0 years ago by l.nilse0
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Comment: C: UniProt.ws report 1:many mappings in a single row
... Together with match() this is a nice solution. Avoids me calling select() multiple times. Thanks a lot for this, Jim and Martin.  ...
written 3.0 years ago by l.nilse0
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Answer: A: UniProt.ws report 1:many mappings in a single row
... My UNIPROT keys are not necessarily unique (in your example they are: Q12345, R4543, T96874), i.e. split/collapse will not work. I had hoped for a multiVals parameter (first, CharacterList, ...) in select() as is available in the mapIds() interface. https://bioconductor.org/packages/release/bioc/ht ...
written 3.1 years ago by l.nilse0
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UniProt.ws report 1:many mappings in a single row
... I am using UNIPROTKB keys to retrieve KEGG entries. Often multiple KEGG entries are found for the same key, resulting in a select() result with more rows than keys. 'select()' returned 1:many mapping between keys and columns Is it possible to get multiple KEGG entries in the same row, i.e. number ...
annotation uniprot.ws uniprot written 3.1 years ago by l.nilse0

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Scholar 3.1 years ago, created an answer that has been accepted. For A: UniProt.ws report 1:many mappings in a single row

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