Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 19k
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United States
Website:
http://bioconductor.org/
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8 hours ago
Joined:
11 years, 2 months ago
Email:
m************@roswellpark.org

Posts by Martin Morgan

<prev • 2,302 results • page 1 of 231 • next >
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Comment: C: bamsignals - bamcoverage has no strand-specific option??
... Just a note that the original question sent email to the maintainer, who had an autoreply generating a comment on the original question that noted that they were out of the office until (23 January?) which generated an email to the maintainer which generated an autoreply... and drastic steps were ta ...
written 11 hours ago by Martin Morgan ♦♦ 19k
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Answer: A: [bug] Wrong protein sequence fetched with R's Biostrings readDNAStringSet functi
... It's a protein sequence, so use `readAAStringSet()`. > Biostrings::readAAStringSet("tmp.fa") A AAStringSet instance of length 1 width seq names [1] 422 MRHIAHTPRGSCFMALLLLLLLA...LHWYANALYKVKDYVLPKSWRHD HH_DROHY_P56674 When re ...
written 11 hours ago by Martin Morgan ♦♦ 19k
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Answer: A: searching for edgeR version 2.2.6
... Bioconductor has 'release' versions tied to versions of R. edgeR 2.2.6 was in Bioconductor release 2.8. From this page, Bioconductor 2.8 was based on R 2.13. It was released in April, 2011 -- this is a very very old version of the software, and it is important to ask what the justification is for us ...
written 15 hours ago by Martin Morgan ♦♦ 19k
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Answer: A: Problems with RSQLite compilation
... It's not really clear why Rcpp is not being found (it is a dependency of RSQLite, and R would have installed it if it were not already installed). You could try re-installing it first biocLite("Rcpp") biocLite("RSQLite") ...
written 5 days ago by Martin Morgan ♦♦ 19k
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Comment: C: Problems with RSQLite compilation
... I disagree with Lluis, it is standard practice to install all packages with biocLite() -- it does no harm in general, and is essential for Bioconductor packages. It's true that RSQLite isn't a Bioconductor package, and that the problem is not technically 'ours', but I guess you're trying to install ...
written 5 days ago by Martin Morgan ♦♦ 19k
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Comment: C: Problem to install "flowClust"
... It's a Bioconductor package so from the package landing page source("https://bioconductor.org/biocLite.R") biocLite("flowClust") ...
written 6 days ago by Martin Morgan ♦♦ 19k
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Comment: C: Best way to create a VRanges object from a large VCF file?
... Did you use ScanVcfParam() to selectively import only the information that you need? Also, for smoe use cases there are readGeno() and similar. ...
written 7 days ago by Martin Morgan ♦♦ 19k
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Comment: C: Installation of package DESeq2
... Not writeable means that the library (directory) where survival was installed is not owned by the account running biocLite(). Probably this means that 'recommended' packages were installed using an administrator account. You could (a) ignore it; (b) run R and update survival under an administrator a ...
written 8 days ago by Martin Morgan ♦♦ 19k
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Answer: A: Installation of package DESeq2
... Solve the first problem -- RCurl -- first. You're on the right track with the system dependency; you'll also need, e.g., $ sudo apt-get install libcurl4-openssl-dev and then > biocLite("RCurl") ...
written 8 days ago by Martin Morgan ♦♦ 19k
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Answer: A: about the use of subsetByFilter()
... The filter argument is supposed to be a FilterRules object, so subsetByFilter(vcf, filter=FilterRules(list(AFADfilter=AFADfilter))) ...
written 10 days ago by Martin Morgan ♦♦ 19k

Latest awards to Martin Morgan

Scholar 9 months ago, created an answer that has been accepted. For A: ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
Scholar 9 months ago, created an answer that has been accepted. For A: ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
Appreciated 9 months ago, created a post with more than 5 votes. For Updated Bioconductor Package Submission Policy
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Filtering a BAM file using RSamtools
Popular Question 9 months ago, created a question with more than 1,000 views. For Bioconductor core team
Scholar 10 months ago, created an answer that has been accepted. For A: How to access Emsembl plants with biomaRt
Scholar 10 months ago, created an answer that has been accepted. For A: How to access Emsembl plants with biomaRt
Scholar 10 months ago, created an answer that has been accepted. For A: How to access Emsembl plants with biomaRt
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Filtering a BAM file using RSamtools
Scholar 10 months ago, created an answer that has been accepted. For A: How to access Emsembl plants with biomaRt
Scholar 10 months ago, created an answer that has been accepted. For A: How to access Emsembl plants with biomaRt
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Filtering a BAM file using RSamtools
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Filtering a BAM file using RSamtools
Scholar 11 months ago, created an answer that has been accepted. For A: How to access Emsembl plants with biomaRt
Scholar 11 months ago, created an answer that has been accepted. For A: How to access Emsembl plants with biomaRt
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Bootstrap confidence intervals on RNA-seq expression from Kallisto
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Filtering a BAM file using RSamtools
Scholar 12 months ago, created an answer that has been accepted. For A: How to access Emsembl plants with biomaRt
Scholar 12 months ago, created an answer that has been accepted. For A: How to access Emsembl plants with biomaRt
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Filtering a BAM file using RSamtools
Appreciated 12 months ago, created a post with more than 5 votes. For Updated Bioconductor Package Submission Policy
Scholar 13 months ago, created an answer that has been accepted. For A: How to access Emsembl plants with biomaRt
Scholar 14 months ago, created an answer that has been accepted. For A: How to access Emsembl plants with biomaRt
Scholar 14 months ago, created an answer that has been accepted. For A: Concatenation of Bimap
Scholar 14 months ago, created an answer that has been accepted. For A: getting the longest transcript by gene from Refseq

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