Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 21k
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http://bioconductor.org/
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11 hours ago
Joined:
12 years, 7 months ago
Email:
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Posts by Martin Morgan

<prev • 2,839 results • page 1 of 284 • next >
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Answer: A: Installing package BiocParallel failed
... The 'devel' software repository was 'flushed' (all packages removed then repopulated) so that packages would include a Date/Published: field inserted by the nightly builder. Unfortunately, package that fail to build do not get pushed to the flushed repository, and BiocParallel had a timeout on the n ...
written 2 days ago by Martin Morgan ♦♦ 21k
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Answer: A: How i can get a list of KEGG pathways and its list of genes?
... Here I use KEGGREST for KEGG information, and org.Hs.eg.db for symbol mapping. The tidyverse is convenient for working with data.frames library(KEGGREST) library(org.Hs.eg.db) library(tidyverse) ## dplyr::select() vs. AnnotationDbi::select() ! These are the KEGG pathways and their Entrez gene id ...
written 5 days ago by Martin Morgan ♦♦ 21k
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Comment: C: Rhdf5 C-library out of date
... I opened an issue at https://github.com/grimbough/rhdf5/issues/18 for the more technically minded... ...
written 6 days ago by Martin Morgan ♦♦ 21k
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Comment: C: GO.db installation fails (MacOS, AnnotationDbi, R3.5.0)
... Glad that worked, can you provide me with the output of .libPaths() and sapply(.libPaths(), function(elt) "AnnotationDbi" %in% dir(elt)) ? it will help to debug this further. ...
written 8 days ago by Martin Morgan ♦♦ 21k
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Comment: C: GO.db installation fails (MacOS, AnnotationDbi, R3.5.0)
... Can you investigate where AnnotationDbi is installed, e.g., looking at something like sapply(.libPaths(), function(elt) "AnnotationDbi" %in% dir(elt)) I don't really know where this will lead, but I would guess that you have two or more .libPaths(), that AnnotationDbi is in a path different from ...
written 10 days ago by Martin Morgan ♦♦ 21k
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Answer: A: GO.db installation fails (MacOS, AnnotationDbi, R3.5.0)
... Did you try to install the missing dependency (this shouldn't usually be necessary, but that is what R says is the problem...)? biocLite("AnnotationDbi") # if this is successful, then... biocLite("GO.db") (Usually one could install multiple packages via biocLite(c("AnnotationDbi", "GO.db")), but ...
written 10 days ago by Martin Morgan ♦♦ 21k
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Answer: A: Fail to download package "TxDb.Mmusculus.UCSC.mm10.ensGene"
... The first error to occur is ** byte-compile and prepare package for lazy loading Error: package or namespace load failed for 'GenomicFeatures' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'stringi' so you should tackle that. You could treat the ...
written 13 days ago by Martin Morgan ♦♦ 21k
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Comment: C: Biobase exprs() method for GeneFeatureSet class
... Hello fmarchildo! Questions similar to yours can already be found at: exprs function - clash with dplyr We have closed your question to allow us to keep similar content in the same thread. If you disagree with this please tell us why in a reply below. We'll be happy to talk abo ...
written 13 days ago by Martin Morgan ♦♦ 21k
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Comment: C: exprs function - clash with dplyr
... The conflicted package forces one to resolve conflicts, and might be a 'best practice'. ...
written 13 days ago by Martin Morgan ♦♦ 21k
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Comment: C: Invitation to submit articles to the Bioconductor gateway on F1000Research
... I opened an issue on github https://github.com/Bioconductor/BioC2018/issues/9 if you want to make a more explicit suggestion. ...
written 13 days ago by Martin Morgan ♦♦ 21k

Latest awards to Martin Morgan

Scholar 4 weeks ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Eliminating repetitive calls to ExperimentHub
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 11 months ago, created an answer that has been accepted. For A: Setting ExperimentHub Cache Location
Scholar 11 months ago, created an answer that has been accepted. For A: Extracting sequences from BSgenomeViews object
Scholar 11 months ago, created an answer that has been accepted. For A: annotation: how to use "character" for function 'select()'
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Rsamtools use for R version 3.4.1
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Import gff from character?
Scholar 11 months ago, created an answer that has been accepted. For A: Warnings messages can not we handles/hidden
Scholar 11 months ago, created an answer that has been accepted. For A: Error building R Markdown v2 document
Scholar 11 months ago, created an answer that has been accepted. For A: How to initialize a SummarizedExperiment?
Scholar 11 months ago, created an answer that has been accepted. For A: about filtering variants in a VCF file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to convert a GRangesList object into a GRanges object?
Scholar 11 months ago, created an answer that has been accepted. For A: Cannot install CummeRbund on R version 3.0.2 (2013-09-25)
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: about filtering variants in a VCF file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Does Rhtslib currently work on Windows?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Setting ExperimentHub Cache Location
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Filtering a BAM file using RSamtools
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Error in GRanges: could not find symbol "recursive" in environment of the generi
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Scholar 11 months ago, created an answer that has been accepted. For A: Error with MSA package - could not find symbol "recursive"
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to access Emsembl plants with biomaRt
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3

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