User: Peter Hickey

gravatar for Peter Hickey
Peter Hickey440
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Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Website:
http://www.peterhickey...
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PeteHaitch
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1 week, 4 days ago
Joined:
6 years, 1 month ago
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Posts by Peter Hickey

<prev • 86 results • page 1 of 9 • next >
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Comment: C: A parser for Tiled Data File (TDF) format?
... Using `normalizePath()` worked. Thanks, Henrik! ...
written 14 days ago by Peter Hickey440
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Comment: C: A parser for Tiled Data File (TDF) format?
... I think this means TDFUtils exists in the .jar file, but I'm pretty outside my knowledge here. $ jar tf ~/miniconda3/share/igvtools-2.3.93-0/igvtools.jar | grep TDFUtils org/broad/igv/tdf/TDFUtils.class ...
written 14 days ago by Peter Hickey440
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Comment: C: A parser for Tiled Data File (TDF) format?
... Do you know if this trick still works, Henrik? I can't get it working on my machine but the combination of rJava, a conda-installed igvtools, and an the general lack of documentation on TDF makes me unsure where the fault lies. library(rJava) .jinit(classpath="~/miniconda3/share/igvtools-2.3.93-0/i ...
written 14 days ago by Peter Hickey440
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Comment: C: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... Why is it beneficial to store the data as a single Rle in SolidRleArraySeed? I think it's more the case that this is a simpler object to design and program with (Hervé Pagès will know best). Doesn't that limit to the total size of the matrix since it spans all columns? Yes, I think so. If yo ...
written 6 weeks ago by Peter Hickey440
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Comment: C: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... suppressPackageStartupMessages(library(S4Vectors)) suppressPackageStartupMessages(library(DelayedArray)) nrow <- 200L ncol <- 5L # Generate some data that can be efficiently run length encoded. x <- Rle(500L + sort(rpois(nrow * ncol, 10))) x #> integer-Rle of length 1000 with 21 runs # ...
written 6 weeks ago by Peter Hickey440
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Answer: A: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... I'm going to assume we're talking about representing 2-dimesionsal arrays. It comes down to how the data are stored (i.e. run length encoded): A DataFrame with Rle columns is run length encoded column-wise with a separate Rle per column. A SolidRleArraySeed-backed DelayedArray is run length enc ...
written 6 weeks ago by Peter Hickey440
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Comment: C: Recommendations for combining multiple 10x runs into one SingleCellExperiment
... Thanks, Aaron. Very helpful (as always). ...
written 7 weeks ago by Peter Hickey440
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Recommendations for combining multiple 10x runs into one SingleCellExperiment
... I've got an experiment with eight 10x scRNA-seq runs that I'm analysing by starting with something based on the simpleSingleCell workflow. I constructed each SingleCellExperiment with DropletUtils::read10xCounts(). I'm looking for any opinions or advice on when to combine these into one SingleCellE ...
simplesinglecell singlecellexperiment dropletutils written 7 weeks ago by Peter Hickey440 • updated 7 weeks ago by Aaron Lun21k
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Comment: C: Minfi error when using force=TRUE in read.metharray
... I believe this is cross-posted from https://github.com/hansenlab/minfi/issues/173. Based on the sessionInfo() you posted there, you are using an old version of minfi. As recommended in http://www.bioconductor.org/help/support/posting-guide/, please try updating to the latest version (see http://www. ...
written 3 months ago by Peter Hickey440
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Comment: C: Minfi error when using force=TRUE in read.metharray
... Please include the output of sessionInfo() otherwise we don't know what version of R or minfi you are using. Please also read http://www.bioconductor.org/help/support/posting-guide/ for advice on creating a question that will be easier for people to help you answer. ...
written 3 months ago by Peter Hickey440

Latest awards to Peter Hickey

Scholar 10 weeks ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Supporter 10 weeks ago, voted at least 25 times.
Popular Question 10 weeks ago, created a question with more than 1,000 views. For VariantAnnotation::readVcf is reordering the FORMAT field of my VCF file
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: From RleList to RleArray
Scholar 6 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Popular Question 6 months ago, created a question with more than 1,000 views. For VariantAnnotation::readVcf is reordering the FORMAT field of my VCF file
Popular Question 17 months ago, created a question with more than 1,000 views. For Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Error when generate mapToGenome
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: From RleList to RleArray
Scholar 17 months ago, created an answer that has been accepted. For A: About methylation data processing
Scholar 17 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Popular Question 17 months ago, created a question with more than 1,000 views. For Unable to load/install rtracklayer (v1.33.2) on OS X (possibly SSL-related?)
Scholar 18 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 2.8 years ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 2.8 years ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq

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