Moderator: Sean Davis

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Sean Davis20k
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Posts by Sean Davis

<prev • 2,058 results • page 1 of 206 • next >
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Answer: A: Error in "getGSEDataTables" in GSEquery package
... Sorry I missed this question the first time.  The solution is to upgrade to GEOquery 2.40 or higher due to a change at NCBI from "http" to "https".  ...
written 9 weeks ago by Sean Davis20k
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Comment: C: CollapsedVCF and ExpandedVCF rownames and vcfs with large ref/alt columns
... Thanks, Val.  row.names=FALSE is a good solution for our use case. If unique IDs are of interest, hashing approaches would be potentially interesting to folks, but perhaps that is best left as a user-level decision. Part of my rationale for asking was to see what others thought.  ...
written 9 weeks ago by Sean Davis20k
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CollapsedVCF and ExpandedVCF rownames and vcfs with large ref/alt columns
... With some newer VCF files, particularly those that have come from structural variant callers, the rownames of the resulting `VCF` objects (when the ID column is missing) can become problematic or excessively large. To give a concrete example, we have VCFs with insertions of dozens or hundreds of bas ...
variantannotation vcf written 9 weeks ago by Sean Davis20k • updated 9 weeks ago by Valerie Obenchain ♦♦ 5.9k
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Comment: C: Reading files from Softlayer Object Storage
... https://github.com/IBMDataScience/objectStoreR/issues/2 ...
written 12 weeks ago by Sean Davis20k
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Answer: A: Reading files from Softlayer Object Storage
... The objectStoreR package is VERY specific in that it only deals with CSV files. As a simple starting place, you could contact the author and ask if he/she is willing to write a objectstore.fetchToDisk() function that simply grabs an object and writes it to disk.  That would allow you to interface wi ...
written 12 weeks ago by Sean Davis20k
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Comment: C: How to start CrispRVariants with fastq file starting point
... Is there a reason that you cannot start at section 2.2 of that user guide?  I believe that section assumes that you have fastq files already. ...
written 12 weeks ago by Sean Davis20k
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Problem with VariantAnnotation and VCF "R" genotype fields when expanding CollapsedVCF
... I noticed a numeric difference between the AD geno field when going from a CollapsedVCF to ExpandedVCF.  Here is an example.  I can share the VCF offline, as it is human data.  In the example, it seems that after expansion, the AD numbers appear to not match the CollapsedVCF version.   > vcfCom ...
bug variantannotation written 12 weeks ago by Sean Davis20k • updated 11 weeks ago by Valerie Obenchain ♦♦ 5.9k
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Answer: A: GEOquery error in downloading SOFT files
... An upgrade to GEOquery 2.40 will likely fix the problem.  NCBI has moved away from using "http" in favor of "https", so you'll need to update GEOquery to address that issue.  Sorry for the inconvenience!   ...
written 3 months ago by Sean Davis20k
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Comment: C: GEOquery Fails to Download Series Matrix File
... Unfortunately, we (bioconductor) do not maintain the conda repo for bioconductor.  It would be up to the conda package maintainer to 1) make sure that the most updated version of R is available and 2) that Bioc package versions match and are updated.   ...
written 3 months ago by Sean Davis20k
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Answer: A: GEOquery Fails to Download Series Matrix File
... Great question.  Sorry for the inconvenience, but NCBI recently changed all `http` links to be `https` only. You'll need to upgrade to at least 2.40 version of GEOquery; this version is associated with the 3.4 release of Bioconductor.  Prior to that, GEOquery used `http` and that is the issue you ar ...
written 3 months ago by Sean Davis20k

Latest awards to Sean Davis

Popular Question 10 months ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Appreciated 10 months ago, created a post with more than 5 votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Popular Question 10 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Popular Question 10 months ago, created a question with more than 1,000 views. For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Scholar 10 months ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Popular Question 10 months ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 10 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Scholar 13 months ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: very high adjusted P-vals using Illumina data from GEO
Voter 13 months ago, voted more than 100 times.
Appreciated 15 months ago, created a post with more than 5 votes. For Bioc2015 conference ongoing now.
Appreciated 19 months ago, created a post with more than 5 votes. For A: differential gene expression
Student 20 months ago, asked a question with at least 3 up-votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Scholar 2.0 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Scholar 2.0 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
Supporter 2.1 years ago, voted at least 25 times.
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: differential gene expression
Scholar 2.3 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Scholar 2.3 years ago, created an answer that has been accepted. For A: Processing RAW CEL files from GEO
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
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