Admin: Valerie Obenchain

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Valerie Obenchain ♦♦ 5.9k
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Posts by Valerie Obenchain

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Comment: C: Easy way to turn OrgDb object from AnnotationHub into package?
... Right. Thanks Jim. Val ...
written 19 days ago by Valerie Obenchain ♦♦ 5.9k
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Answer: A: Feature request: columns and keytypes of organism packages in vignette
... Hi Mike, I agree, this would be a good addition. The OrganismDbi parent package does have a vignette that demos keys/columns etc. but the individual packages (Homo.sapiens) don't have vignettes. We are a little short staffed right now but maybe someone from the community would like to contribute a ...
written 19 days ago by Valerie Obenchain ♦♦ 5.9k
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Answer: A: Easy way to turn OrgDb object from AnnotationHub into package?
... Hi Jenny, The OrgDb object is essentially the sqlite file and you can make a package from the sqlite with AnnotationForge::makeAnnDbPkg(). See the man page example for creating a 'seed' then giving the seed and the path to the sqlite to makeAnnDbPkg(). As the PkgTemplate arg use NCBIORG.DB. See all ...
written 19 days ago by Valerie Obenchain ♦♦ 5.9k
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Comment: C: Getting errors with makeTxDbFromBiomart
... makeTxDbFromBiomart() uses biomaRt under the hood so, yes, it supports these sister ensembl sites. You can specify different hosts with the 'host' argument, also see the 'biomart' and 'dataset' arguments on the ?makeTxDbFromBiomart man page. > listMarts(host="plants.ensembl.org") bi ...
written 27 days ago by Valerie Obenchain ♦♦ 5.9k
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Comment: C: How to get GenomicAlignments to read all reads?
... If the workflow Martin suggests doesn't shed any light I can look at the files for you. Make the files (or subsets) available to valerie.obenchain@roswellpark.org.  Valerie ...
written 28 days ago by Valerie Obenchain ♦♦ 5.9k
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Comment: C: package 'ChAMP' demo/test code fails at champ.CNA()
... This thread is old - please post a new question with the code you've tried and your sessionInfo(). Tag the question with 'ChAMP.  Valerie ...
written 29 days ago by Valerie Obenchain ♦♦ 5.9k
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Answer: A: mismatch between AnnotationHub ensembl v71 hsapiens and direct download using rt
... Hi, Prior to July 2016, the GTF files from Ensembl were pre-built and stored in S3 (versions <=83). Once built they are not updated unless a bug is reported. The date of the GTF 71 files in the S3 bucket is November 2013. As of July 2016, there is no pre-building of the GTF (versions >=84) T ...
written 4 weeks ago by Valerie Obenchain ♦♦ 5.9k
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Answer: A: genomicAlignments: fail to run readGAlignments example code
... I cannot reproduce this error. Are you still having this problem? Valerie ...
written 5 weeks ago by Valerie Obenchain ♦♦ 5.9k
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Comment: C: `precede` does not perform as expected
... After some discussion, the following changes were made to precede() and follow() in GenomicRanges 1.27.21: 1) The 'select' argument has been made consistent with the methods in IRanges: precede() now supports select=c("first", "all") and follow() supports select=c("last", "all"). 2) When 'x' is '* ...
written 5 weeks ago by Valerie Obenchain ♦♦ 5.9k
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Comment: C: about collapsed and expanded vcf file
... The ExpandedVCF class is a flat-ish form of the CollapsedVCF. The expansion is centered around the ALT field. Often there can be more than one ALT value per variant and in the CollapsedVCF all ALT values for a single variant are presented in a single row. While there is one row per genomic position, ...
written 6 weeks ago by Valerie Obenchain ♦♦ 5.9k

Latest awards to Valerie Obenchain

Teacher 29 days ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 29 days ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: readGAlignmentPairs slow in problematic region
Scholar 10 months ago, created an answer that has been accepted. For A: BiocParallel example does not work any more (sbatch produced exit code 1)
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Genomic features for genomic positions
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: AnnotationHub: two broad peaks from same url are not the same
Appreciated 10 months ago, created a post with more than 5 votes. For New Package Submission Process
Scholar 10 months ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Scholar 10 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 10 months ago, created an answer that has been accepted. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 10 months ago, created an answer that has been accepted. For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
Scholar 10 months ago, created an answer that has been accepted. For A: AnnotationHub: two broad peaks from same url are not the same
Scholar 10 months ago, created an answer that has been accepted. For A: Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowP
Scholar 10 months ago, created an answer that has been accepted. For A: Genomic features for genomic positions
Scholar 10 months ago, created an answer that has been accepted. For A: GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Scholar 10 months ago, created an answer that has been accepted. For A: Intersecting a Granges and a GRangesList using within
Scholar 11 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Guru 11 months ago, received more than 100 upvotes.
Scholar 13 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 13 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Appreciated 13 months ago, created a post with more than 5 votes. For October Newsletter now available
Scholar 14 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 15 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 15 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix

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