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Admin: Martin Morgan

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Martin Morgan ♦♦ 22k
Reputation:
22,490
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Trusted
Location:
United States
Website:
http://bioconductor.org/
Last seen:
14 hours ago
Joined:
13 years, 3 months ago
Email:
m************@gmail.com

Posts by Martin Morgan

<prev • 3,056 results • page 2 of 306 • next >
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Comment: C: mclapply to loop over a GRangesList object
... I don't think that's any faster than ``` mclapply(GRsList, gaps, mc.cores = 4) ``` ? The 'cost' is in creating a `GRanges()` for each element of the list, the cost is paid either internally by `lapply()` or explicitly by `GRsList[[i]]`, and either way distributed across cores. The 'Bioconductor' wa ...
written 15 days ago by Martin Morgan ♦♦ 22k
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Comment: C: mclapply to loop over a GRangesList object
... Then you're looking for `GenomicFeatures::intronsByTranscript()`! ...
written 16 days ago by Martin Morgan ♦♦ 22k
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Answer: A: mclapply to loop over a GRangesList object
... Depending on what your goal is, a fast approach is to 'unlist-apply-relist' ```r gr = unlist(grl) gr$foo = ... relist(gr, grl) ``` Probably describing what you would like to do, in not too much detail, would lead to a more helpful answer. ...
written 16 days ago by Martin Morgan ♦♦ 22k
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Comment: C: DESeq2 Dose not work
... Start at the first error > library(DESeq2, quietly=T) Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘rlang’ and fix it (by installing rlang). ...
written 16 days ago by Martin Morgan ♦♦ 22k
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Answer: A: Splicing large bam file with Rsamtools
... I'm not exactly sure what you mean by 'fill in the position and qwidth'. It's possible to find the widths of each chromosome with `Rsamtools::scanBamHeader()`, and use these to create GRanges corresponding to each seqname (chromosome). Instead of using `scanBam()`, use the [GenomicAlignments][1] pa ...
written 19 days ago by Martin Morgan ♦♦ 22k
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Answer: A: Bioconductor IP addresses for whitelist
... master.bioconductor.org is in the Amazon cloud, but 52.71.54.154 is a static (elastic) IP address; it is stable. An alternative is to clone, [using rsync][1], the Bioconductor (and/or CRAN) repository and arrange for your cluster to point to the local repository (via `R.home("etc/Rprofile.site")`, ...
written 20 days ago by Martin Morgan ♦♦ 22k
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Answer: A: How to work with dplyr verbs in the colData slot of SingleCellExperiment objects
... These S4 objects are based on 'DataFrame', so > colData(sce) = as(colData(sce), "DataFrame") Or > colData(sce) = colData(sce) %>% as.data.frame() %>% etc... %>% DataFrame() ...
written 23 days ago by Martin Morgan ♦♦ 22k
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Comment: C: error in makeTxDbFromUCSC
... Do NOT post in multiple places; all locations are monitored by the same people. ...
written 24 days ago by Martin Morgan ♦♦ 22k
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Answer: A: standardChromosomes says EOF within quoted string
... Thank you for the clear example. Please check that your installation is current -- `BiocManager::valid()` -- I believe GenomeInfoDb is at version 1.18.1. ...
written 26 days ago by Martin Morgan ♦♦ 22k
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Comment: C: error in makeTxDbFromUCSC
... Please resist the temptation to post in multiple locations (I think you got them all, here, bioc-devel, [GitHub][1], and the maintainer email address)! This seems to have been reported before https://support.bioconductor.org/p/114901/ https://support.bioconductor.org/p/107839/ . We'll work on this ...
written 26 days ago by Martin Morgan ♦♦ 22k

Latest awards to Martin Morgan

Appreciated 11 weeks ago, created a post with more than 5 votes. For Statistics and Computing in Genome Science (CSAMA) Course Material
Scholar 3 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 3 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
Teacher 3 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
Teacher 3 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
Scholar 4 months 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 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
Teacher 4 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
Scholar 4 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 6 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Teacher 6 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
Popular Question 8 months ago, created a question with more than 1,000 views. For Updated Bioconductor Package Submission Policy
Scholar 8 months ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Popular Question 8 months ago, created a question with more than 1,000 views. For BioC 2015 Annual Conference
Teacher 8 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 8 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
Scholar 8 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Good Answer 8 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
Scholar 8 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 9 months ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Eliminating repetitive calls to ExperimentHub
Teacher 9 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
Scholar 9 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Scholar 20 months ago, created an answer that has been accepted. For A: about filtering variants in a VCF file

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