User: Ido M. Tamir

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Ido M. Tamir150
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Posts by Ido M. Tamir

<prev • 15 results • page 1 of 2 • next >
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DESeq2 1.2.10 vs 1.5.26
... Hi, I tried to switch from DESeq2_1.2.10 (R3.0) to DESeq2_1.5.26 (R3.1) but it looks like it 1.5.26 is much more aggressive in the shrinking of the variance estimation. The rlog normalized fold changes are also very different. The dataset was generated with dds <- makeExampleDESeqDataSet(n = ...
written 5.4 years ago by Ido M. Tamir150 • updated 5.4 years ago by Michael Love26k
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looking for GRanges ggply like ddply
... Hi, I need to aggregate Granges by metadata I would like to write something like: ggply(granges, .(transcript_id, type), function(tt) { ... }) is this possible? thank you very much, ido ...
written 5.7 years ago by Ido M. Tamir150 • updated 5.7 years ago by Michael Lawrence11k
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Comment: C: makeGappedAlignmentPairs for broken pairs
... Dear Valerie, thank you very much for your reply. I can't test the development packages at the moment, I'm still on 2.12. > param <- ScanBamParam(flag=scanBamFlag(hasUnmappedMate=TRUE)) a) Will this load only reads with unmapped mates or will this allow both proper paired and unpaired which i ...
written 5.9 years ago by Ido M. Tamir150
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makeGappedAlignmentPairs for broken pairs
... Hi, is there a roadmap for allowing paired end reads where only one is mapped to be reported? Basically I would like to have readGappedAlignmentPairs report them also. One could reread the whole file and take only those reads where the makeGappedAlignmentPairs test was unsuccessfull. thank you very ...
written 5.9 years ago by Ido M. Tamir150 • updated 5.9 years ago by Valerie Obenchain6.7k
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Comment: C: known gene => gene symbol for UCSC
... Dear James, thank you very much. It did not work with: a fresh session (a) and an old session (b) Your packages seem newer, but my ids are from the old package, so they should be consistent. I just installed the bioconductor packages Mus.musculus and TxDb.Mmusculus.UCSC.mm10.ensGene today. best, ...
written 6.7 years ago by Ido M. Tamir150
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exonsBy order
... Hi, is it guaranteed that the exons within each of the GRanges resulting from exonsBy are sorted in ascending order? The GRangesList seems unsorted. thank you very much, ido ...
written 6.7 years ago by Ido M. Tamir150 • updated 6.7 years ago by Valerie Obenchain6.7k
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known gene => gene symbol for UCSC
... Hi, how is one supposed to go from ucsc known gene id to gene symbols. > cols(TxDb.Mmusculus.UCSC.mm9.knownGene) [1] "CDSID" "CDSNAME" "CDSCHROM" "CDSSTRAND" "CDSSTART" [6] "CDSEND" "EXONID" "EXONNAME" "EXONCHROM" "EXONSTRAND" [11] "EXONSTART" "EXONEND" "GENEID" " ...
go written 6.7 years ago by Ido M. Tamir150 • updated 6.7 years ago by James W. MacDonald52k
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Mus.musculus package pdf not found
... Hi, I cant get information about the Mus.musculus package. The link on the page is dead http://www.bioconductor.org/packages/2.11/data/annotation/html/Mus.mus culus.html http://www.bioconductor.org/packages/2.11/data/annotation/manuals/Mus. musculus/man/Mus.musculus.pdf best, ido ...
written 6.7 years ago by Ido M. Tamir150 • updated 6.7 years ago by Dan Tenenbaum8.2k
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[Job] Bioinformatician-NGS (Vienna, Austria)
... Bioinformatician-NGS The Campus Science Support Facilities GmbH (CSF) is a non-profit organisation providing scientific infrastructure to the institutions at the Vienna Biocenter. We are seeking an experienced Bioinformatician (m/f) to join the Next Generation Sequencing Unit. Major tasks will be ...
sequencing infrastructure written 8.0 years ago by Ido M. Tamir150
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Answer: A: matrix transformation
... > Dear Mailing List, > > I wrote the following function "matrix2tuple.sf" to translate a "cartesian > xy matrix" as a "tuple matrix", to store it in relational database. The > code works fine for a test set. My problem is, my real matrix is 7000 x > 10000 big, which ends up in 70' ...
written 9.1 years ago by Ido M. Tamir150

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Popular Question 5.4 years ago, created a question with more than 1,000 views. For known gene => gene symbol for UCSC

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