User: Martin Morgan

gravatar for Martin Morgan
Martin Morgan1.5k
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Website:
http://bioconductor.org
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1 month, 1 week ago
Joined:
6 years, 9 months ago
Email:
m*******@fhcrc.org

Posts by Martin Morgan

<prev • 73 results • page 1 of 8 • next >
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Comment: C: R&Bioconductor: Extract coverage from bamfile given GRanges object?
... Careful about what 'coverage' means when exons overlap; maybe you want to ScanBamParam(which=reduce(allExons)) to avoid double counting. ...
written 20 months ago by Martin Morgan1.5k
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Comment: C: Bioconductor as a source for the dependencies of an R package?
... `biocLite("your/amazing")` works too (via devtools), without requiring you to label your package with the biocViews term. It does this by setting the argument `repos` to a value that includes Bioconductor repositories, `BiocInstaller::biocinstallRepos()`, so you can do that, too `install_github("you ...
written 20 months ago by Martin Morgan1.5k
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Job: R / Bioconductor core team Senior Programmer / Analyst
... The Bioconductor team has an opening available for a Senior Progammer / Analyst. Bioconductor is an exciting and reward work environment. You'll be making valuable contributions to this successful, high-profile, well-regarded open-source software project for the analysis and comprehension of high-th ...
R bioconductor jobs written 22 months ago by Martin Morgan1.5k
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Answer: A: bioconductor for R 2.6.2 version
... R 2.6.2 is from 2008. I suggest that you use a more recent version. For very old versions, I *think* you can use source("http://bioconductor.org/getBioC.R") I think also that using install.packages() directly will likely succeed in these very old versions of R / Bioconductor by manually setting t ...
written 2.5 years ago by Martin Morgan1.5k
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Comment: C: Hg19 Coordinate To Cds Position
... @Duff But see GenomicAlignments::mapToAlignments and GenomicFeatures::mapToTranscripts. ...
written 2.6 years ago by Martin Morgan1.5k
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Comment: C: BioC 2015, Bioconductor Annual Conference, July 20-22, Seattle, WA
... Updated, thanks! ...
written 2.6 years ago by Martin Morgan1.5k
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News: BioC 2015, Bioconductor Annual Conference, July 20-22, Seattle, WA
... BioC 2015, the Bioconductor Annual Conference, is taking shape, and registration is open! The conference takes place July 20 (Developer Day), 21, and 22 in Seattle, WA. Please visit the conference web site and registration page for more information. ...
bioconductor conference news written 2.6 years ago by Martin Morgan1.5k
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Comment: C: How can I filter a vcf file by DP and GQ using the R package VariantAnnotation?
... To fix your code, use '&' (vector and) rather than '&&' (scalar and) as in response to your other version of this question. ...
written 2.7 years ago by Martin Morgan1.5k
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Answer: A: How to get gene names from CpG islands coordinates with R/Bioconductor
... Consider asking questions about Bioconductor packages on the Bioconductor support forum. Load the mouse ensGene 'TxDb' package, and get gene coordinates library(TxDb.Mmusculus.UCSC.mm10.ensGene) genes = genes(TxDb.Mmusculus.UCSC.mm10.ensGene) Coerce your data.frame to a GRanges object, maybe wit ...
written 2.7 years ago by Martin Morgan1.5k
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Answer: C: Rsubread installation issues
... See https://support.bioconductor.org/p/65429/ ...
written 2.7 years ago by Martin Morgan1.5k

Latest awards to Martin Morgan

Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: R Loop In Biostrings
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Updated Affy: Readaffy Has Changed And Breaks My Pipeline!
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Parsing Variants From 1000 Genomes Data
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Comparing Order Of Genes In Two Lists Using Orderedlist
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: How to get the version history of a bioconductor package
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Parsing Variants From 1000 Genomes Data
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Parsing Variants From 1000 Genomes Data
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Parsing Variants From 1000 Genomes Data
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: R Loop In Biostrings
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Parsing Variants From 1000 Genomes Data
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Updated Affy: Readaffy Has Changed And Breaks My Pipeline!
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Parsing Variants From 1000 Genomes Data
Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For A: R Loop In Biostrings
Scholar 3.0 years ago, created an answer that has been accepted. For A: Calculating Intron relative distribution
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Parsing Variants From 1000 Genomes Data
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Parsing Variants From 1000 Genomes Data
Scholar 3.3 years ago, created an answer that has been accepted. For A: Calculating Intron relative distribution
Voter 3.4 years ago, voted more than 100 times.
Scholar 3.5 years ago, created an answer that has been accepted. For A: Calculating Intron relative distribution
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Parsing Variants From 1000 Genomes Data
Guru 3.5 years ago, received more than 100 upvotes.
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Parsing Variants From 1000 Genomes Data
Appreciated 4.1 years ago, created a post with more than 5 votes. For A: Parsing Variants From 1000 Genomes Data
Appreciated 4.1 years ago, created a post with more than 5 votes. For A: R Loop In Biostrings
Appreciated 4.1 years ago, created a post with more than 5 votes. For A: All Children, Grand Children Of Go Id

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