Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 21k
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Website:
http://bioconductor.org/
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1 day, 22 hours ago
Joined:
12 years, 3 months ago
Email:
m************@roswellpark.org

Posts by Martin Morgan

<prev • 2,730 results • page 1 of 273 • next >
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Comment: C: Problem in reading .bam files (aligned to transcriptome) with ribofileCR functio
... Yes, the file path is somehow incorrect. You could try file.choose() to select the file that you are interested in, or file.exists('/Users/bsad/Documents/PhD/polysome_data/NGS_attempt_Footprints_only/[UCSC_Main_on_Human__refGene_(genome)].fasta') to test whether the file actually exists. Also, the u ...
written 2 days ago by Martin Morgan ♦♦ 21k
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Comment: C: Problem in reading .bam files (aligned to transcriptome) with ribofileCR functio
... Usually the best strategy is to simplify your code to the bare minimum required to produce the error, and then to report (cut and paste) the error into the question. If you really wrote the commands as above, then a guess would be that your BAM files (not fasta files) are really not at ~/Users/PATH_ ...
written 2 days ago by Martin Morgan ♦♦ 21k
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Answer: A: bplapply with ShortRead functions
... Does it help to use SnowParam() instead of MulticoreParam() ? Otherwise, I think the processes may be accessing shared global variables in an unhealthy way. ...
written 4 days ago by Martin Morgan ♦♦ 21k
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Answer: A: pkgDepTools does not consider LinkingTo: fields
... Thanks; fixed in 1.45.1. For future issues, I create a github repository for this package. ...
written 7 days ago by Martin Morgan ♦♦ 21k
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Comment: C: HDF5 reading speed
... This isn't a particularly good example because 'toy.h5' is small, but fl = system.file(package="HDF5Array", "extdata", "toy.h5") f0 = function() hdf5load(fl, load=FALSE, verbosity=0, tidy=TRUE) f1 = function() h5read(fl, "/") microbenchmark(f0(), f1(), times=5) Leads to > microbenchmark(f0() ...
written 10 days ago by Martin Morgan ♦♦ 21k
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Comment: C: Failure to update BiocGenerics in Ubuntu 17.10 from 0.22.1 to 0.23 and higher
... Use the 'comment' button instead of 'answer'. I messed up my quotations in the original comment, and have fixed them -- R --vanilla -e '<foo>' starts R without loading .Rprofile / .Renvir / .RData files and then executes the R command <foo>. Glad that you arrived at solution anyway. ...
written 15 days ago by Martin Morgan ♦♦ 21k
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Comment: C: Failure to update BiocGenerics in Ubuntu 17.10 from 0.22.1 to 0.23 and higher
... Be sure to update packages in a 'vanilla' R session with no additional packages attached, e.g., from the comman line R --vanilla -e 'BiocInstaller::biocLite("BiocGenerics")' If that fails the next level of solution is to update R to the current version, R-3.4.3; the 'hotfix' referenced in the err ...
written 15 days ago by Martin Morgan ♦♦ 21k
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Comment: C: Failure to update BiocGenerics in Ubuntu 17.10 from 0.22.1 to 0.23 and higher
... What is the output of source("https://bioconductor.org/biocLite.R") biocLite("BiocGenerics")   ...
written 15 days ago by Martin Morgan ♦♦ 21k
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Comment: C: Beachmat install / compile issue
... I think that the paths above are dynamically determined; if they're wrong then LD_LIBRARY_PATH=... ldd beachmat.so might do the right thing, where the path is to the location of the correct libraries. ...
written 16 days ago by Martin Morgan ♦♦ 21k
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Answer: A: is the Rsamtools::pileup example broken?
... Nice question! the problem is that the base qualities of the reads in the example file are, for some reason, low quality, so they fail to pass the min_base_quality default of PileupParam(). So... > fl <- RNAseqData.HNRNPC.bam.chr14_BAMFILES[1] > param <- PileupParam(min_base_quality = ...
written 16 days ago by Martin Morgan ♦♦ 21k

Latest awards to Martin Morgan

Scholar 7 months ago, created an answer that has been accepted. For A: BiocParallel: messages shown only when processes finished
Teacher 8 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
Scholar 8 months ago, created an answer that has been accepted. For A: BiocParallel: messages shown only when processes finished
Scholar 8 months ago, created an answer that has been accepted. For A: BiocParallel: messages shown only when processes finished
Scholar 8 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 8 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 8 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Error in GRanges: could not find symbol "recursive" in environment of the generi
Appreciated 9 months ago, created a post with more than 5 votes. For Statistics and Computing in Genome Science (CSAMA) Course Material
Scholar 9 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 9 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 9 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Appreciated 10 months ago, created a post with more than 5 votes. For BioC 2015 Annual Conference
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Scholar 10 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 10 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 10 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Appreciated 11 months ago, created a post with more than 5 votes. For BioC 2015 Annual Conference
Scholar 11 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 11 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
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: about the use of subsetByFilter()
Scholar 12 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()

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