User: Paul Leo

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Paul Leo970
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Posts by Paul Leo

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Job in statistical genetics / bioinformatics
... A 3yr Research Fellow position is available at the Queensland Brain Institute (QBI), University of Queensland, Brisbane, Australia. The Research Fellow will be part of the Mowry Group at QBI, whose primary research goal is to identify and functionally characterise susceptibility genes for schizoph ...
sequencing genetics written 6.0 years ago by Paul Leo970
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Job in GWAS / Next Gen Sequencing / genetics
... Bioinformaticians and Statistical Genetics types with experience in GWAS , Next Gen Sequencing or Genetics ? Great job in a terrific location : http://www.seek.com.au/job/25102908 Cheers Paul ...
sequencing genetics written 6.2 years ago by Paul Leo970
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Answer: A: Finding mismatches between reads and reference sequence
... HI David, Probably Herve has answered your question... But about a 1 1/2 ago I wrote some code that : Given a genomic location(s) (a SNP) and some BAM file(s) uses Rsamtools (to get the cigar and the reads in that location) and functions like cigarToQWidth cigarQNarrow to get the bases in each read ...
written 6.6 years ago by Paul Leo970
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Answer: A: R 2.15.2 trouble
... I think the problem is related to: ------------------------- 2: installed directory not writable, cannot update packages 'foreign', 'lattice', 'MASS', 'Matrix', 'nlme', 'rpart', 'survival' -------------- perhaps you have installed R as sudo or superuser so the core 'foreign', 'lattice', 'MASS', ...
written 6.8 years ago by Paul Leo970
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Comment: C: Turning a GRanges Metadata Column into Rle List
... Actually this may be better. than my last post: But making the Rle object of scores using "coverage and weights" (is the only way I could think of). In won't work in cases where the intervals in ir.encode.data are not unique (that is the coverage values must always be one else you get coverage*sc ...
written 6.8 years ago by Paul Leo970
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Comment: C: Turning a GRanges Metadata Column into Rle List
... If you want the maximum of the overlap you can use something like this too: ir<-IRanges(start=you.intervals[,"start"],end=you.intervals[,"end"]) ir.encode.data<-IRanges(start=encode.data[,"start"],end=encode.data[," end"]) over<-findOverlaps(ir,ir.encode.data) query<-queryHits(over) s ...
written 6.8 years ago by Paul Leo970
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Answer: A: seqlevels in VCF objects
... There is a discussion of something similar in the "GenomicRanges Use Cases.pdf" (in the genomicRanges library) see section 3.1 of the pdf: You can change the seqleveles directly: seqlevels(exonRanges) <- newlvls # reorder the levels names(newlvls) <- seqlevels(aligns) Dr Paul Leo Senior ...
written 6.8 years ago by Paul Leo970
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Error in Installing BioBase Development version
... For: R Under development (unstable) (2013-01-02 r61527) -- "Unsuffered Consequences" Copyright (C) 2013 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) Encountered error in installing BioBase: Rinit.c:3:31: error: R_ext/RConverters.h: N ...
written 6.9 years ago by Paul Leo970 • updated 6.9 years ago by Dan Tenenbaum8.2k
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Answer: A: visualizing peptide alignments
... There is the "classic" set of tools for multiple sequence alignment: http://www.clustal.org/ ClustalX for windows, user friendly. There is "probably" an R -interface? -----Original Message----- From: Juliet Hannah To: bioconductor at r-project.org Subject: [BioC] visualizing peptide alignment ...
written 7.0 years ago by Paul Leo970
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Comment: C: About ensembl genes
... HI Chris, That is really just a biology question , there are lots of examples (ok mainly UTR overlaps) but others intron-exon. Articles like: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC139260/ (and others you might get for searching very broadly with "overlapping genes in mouse examples") will he ...
written 7.3 years ago by Paul Leo970

Latest awards to Paul Leo

Popular Question 6.0 years ago, created a question with more than 1,000 views. For Add extra columns to GRanges Metadata
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Add extra columns to GRanges Metadata

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