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Admin: Martin Morgan

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Martin Morgan ♦♦ 23k
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Website:
http://bioconductor.org/
Last seen:
16 minutes ago
Joined:
13 years, 3 months ago
Email:
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Posts by Martin Morgan

<prev • 3,059 results • page 1 of 306 • next >
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Comment: C: How can I install DeSeq2 in Jupyter Notebook?
... Start with the first problem installation of package ‘preprocessCore’ had non-zero exit status and debug that `BiocManager::install("preprocessCore")`; report what the specific problem is here on the mailing list. Consider formatting your code (select and press the little 101010 icon above the ...
written 1 hour ago by Martin Morgan ♦♦ 23k
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Comment: C: caught segfault error when loading S4Vectors package in R
... The packages are CRAN packages. Normally, they can be updated with BiocManager, but likely these packages have system or other dependencies that are preventing their re-installation. The strategy is to try installing each individually and identifying what the problem is. If a 'configure' script runs ...
written 1 hour ago by Martin Morgan ♦♦ 23k
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Comment: C: caught segfault error when loading S4Vectors package in R
... Make sure that your installed packages are from the same release; either BiocManager::valid() # current release or BiocInstaller::biocValid() # older versions It's not clear from your output why you think this is S4Vector's problem? ...
written 3 hours ago by Martin Morgan ♦♦ 23k
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Comment: C: How to read variants into R from large dataset using VariantAnnotation
... Thanks for your patience; VariantAnnotation had expected typical queries not to have as many samples. Please try version 1.28.11, which is available now via BiocManager::install("Bioconductor/VariantAnnotation", ref="RELEASE_3_8") or in 48 hours or so via BiocManager::install("VariantAnno ...
written 4 days ago by Martin Morgan ♦♦ 23k
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Comment: C: indexBam(), summarizeOverlaps() error: RNA-seq
... It might also be that you have unfortunately downloaded the file as 'text' rather than 'binary'. ...
written 4 days ago by Martin Morgan ♦♦ 23k
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Comment: C: How to read variants into R from large dataset using VariantAnnotation
... I will try to look at the code; as a second work-around I wonder if you specify _all_ samples it will also work? rng <- GRanges(seqnames="22", ranges=IRanges(start=16050075,end=16051874)) param <- ScanVcfParam(which=rng,geno="GT",samples = samples(scanVcfHeader(vcf.ref.file))) Is th ...
written 4 days ago by Martin Morgan ♦♦ 23k
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Answer: A: How to read variants into R from large dataset using VariantAnnotation
... Two suggestions. Use the `VariantAnnotation::readGT()` function for a more efficient input. Use as the path to the VCF file a `VcfFile()` with `yieldSize=` some number of variant to read in a chunk; process the file in an iterative fashion, maybe using `GenomicFiles::reduceByYield()`, which implem ...
written 8 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Ranges from a fasta file
... Backing up, what is it that you want to do? I had not read your question carefully enough, and though that you had sequences, e.g., of chromosomes, and you wanted to extract sub-sequences, e.g., of small RNAs, whose genomic coordinates you knew. You could for instance add a column to your GRanges o ...
written 8 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Ranges from a fasta file
... A GRanges has `seqnames()` (e.g., chromsomes) as well as `names()` (e.g., exon IDs). You want to ensure that all(seqnames(gr_obj) %in% names(fasta)) ...
written 8 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Ranges from a fasta file
... The method is actually in BSgenome; sorry for not being clear. ...
written 8 days ago by Martin Morgan ♦♦ 23k

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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