Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 23k
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Website:
http://bioconductor.org/
Last seen:
8 hours ago
Joined:
13 years, 11 months ago
Email:
m************@gmail.com

Posts by Martin Morgan

<prev • 3,252 results • page 1 of 326 • next >
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Comment: C: How to filter out low read counts
... updated `assay()` --> `assays()` ...
written 1 day ago by Martin Morgan ♦♦ 23k
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Comment: C: DEseq2 loading library problem
... It looks like you're missing a package `GenomeInfoDbData`, so you might try ``` BiocManager::install("GenomeInfoDbData")` ``` This might work but a better approach is to ask how you managed to get into a situation where this dependency was not installed? Have you always used `BiocManager::install()` ...
written 1 day ago by Martin Morgan ♦♦ 23k
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Answer: A: How to filter out low read counts
... Note that `assays(data)[["exp_count"]]` is a matrix, so perhaps you are interested in ``` keep <- rowSums(assays(data)[["exp_count"]]) > 1 data_filtered <- data[keep,] ``` ...
written 1 day ago by Martin Morgan ♦♦ 23k
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Comment: C: How to filter out low read counts
... 'Accessors' define how the object is to be manipulated by the user, allowing the developer to chose representations that are efficient for them. For instance, in the Biostrings package ``` > dna = Biostrings::DNAStringSet("AA") > dna@ dna@elementMetadata dna@metadata dna@ranges dna@elem ...
written 1 day ago by Martin Morgan ♦♦ 23k
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Answer: A: DESeq2 installation issue
... You have a version of the package 'BiocVersion' installed from a previous R installation; probably you updated R but re-used the old library. Please see the BiocManager [vignette][1] on options to use a separate library for your new R installation (recommended) or update all packages to the version ...
written 1 day ago by Martin Morgan ♦♦ 23k
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Comment: C: How to filter out low read counts
... Please NEVER use direct slot access `@` and instead use accessors, `assay()` or `assays(data)[[1]]`. ...
written 1 day ago by Martin Morgan ♦♦ 23k
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Comment: C: TxDb.Hsapiens.UCSC.hg38.ensGene doesn't exist
... Several packages make use of AnnotationHub or ExperimentHub resources in a way that is transparent to the user, e.g., including a function like ``` myfun <- function() { AnnotationHub()[["AH123"]] } ``` See the manual [Creating an AnnotationHub Package][1] (But ask questions about package de ...
written 3 days ago by Martin Morgan ♦♦ 23k
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Comment: C: TxDb.Hsapiens.UCSC.hg38.ensGene doesn't exist
... hubs == new data; in some ideal world we'd like the package-based TxDb transitioned to the hubs, too... ...
written 3 days ago by Martin Morgan ♦♦ 23k
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Comment: C: How to build and map to a "pre-mRNA" reference transcriptome for single nucleus
... I think implicit in the question is the desire to do this in or with R / Bioconductor, so the question is appropriate here. ...
written 8 days ago by Martin Morgan ♦♦ 23k
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Comment: C: DESeq2 using many cores despite parallel = FALSE
... you could try `trace(bplapply)` (or maybe `trace(BiocParallel::bplapply)`) before running `estimateSizeFactors()`; you'll see a trace print every time `bplapply()` is evaluated. You could also add an expression to `trace()` to document how `bplapply()` is being called... ``` > trace(bplapply, qu ...
written 8 days ago by Martin Morgan ♦♦ 23k

Latest awards to Martin Morgan

Scholar 11 weeks ago, created an answer that has been accepted. For A: GSEABase: how to extract shortDescription from GeneSetCollection object
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: how does coverage() works
Scholar 11 weeks ago, created an answer that has been accepted. For A: GSEABase: how to extract shortDescription from GeneSetCollection object
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: how does coverage() works
Popular Question 9 months ago, created a question with more than 1,000 views. For BioC 2017: Where Software and Biology Connect, 26 / 27 - 28 July, Boston, MA
Scholar 9 months ago, created an answer that has been accepted. For A: bplapply with ShortRead functions
Appreciated 9 months ago, created a post with more than 5 votes. For Bioconductor Technical Advisory Board
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: RSVSim insertions from chr1 to chr2
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Rsamtools use for R version 3.4.1
Scholar 9 months ago, created an answer that has been accepted. For A: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Best alternative annotation package to BiomaRt
Popular Question 9 months ago, created a question with more than 1,000 views. For Bioconductor Senior Programmer / Analyst
Teacher 9 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 9 months ago, created an answer that has been accepted. For A: how does coverage() works
Scholar 9 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Scholar 9 months ago, created an answer that has been accepted. For A: Ranges from a fasta file
Scholar 9 months ago, created an answer that has been accepted. For A: DataFrame after splitting and back
Scholar 9 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
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: GSEABase: how to extract shortDescription from GeneSetCollection object
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
Scholar 9 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
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

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