User: Peter Hickey
Peter Hickey • 460
- Reputation:
- 460
- Status:
- Trusted
- Location:
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Website:
- http://www.peterhickey...
- Twitter:
- PeteHaitch
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 day, 6 hours ago
- Joined:
- 6 years, 12 months ago
- Email:
- p***********@gmail.com
Posts by Peter Hickey
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... BioCAsia is coming to Sydney on December 5-6.
This will be the fifth Bioconductor Asia meeting.
On December 5 we'll bring together researchers with an interest in Bioconductor and R to exchange ideas and expertise.
On December 6 we're teaming up with BioinfoSummer (Dec 2-6) to run hands on bioinform ...
written 4 months ago by
Peter Hickey • 460
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... Please include a reproducible example, including the output of `BiocManager::valid()` (see https://support.bioconductor.org/info/faq/ for further details).
I can then attempt to help diagnose the issue. ...
written 5 months ago by
Peter Hickey • 460
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... Using `normalizePath()` worked. Thanks, Henrik! ...
written 10 months ago by
Peter Hickey • 460
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... 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 10 months ago by
Peter Hickey • 460
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... 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 10 months ago by
Peter Hickey • 460
1
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...
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 12 months ago by
Peter Hickey • 460
1
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1
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... 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 12 months ago by
Peter Hickey • 460
4
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1
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... 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 12 months ago by
Peter Hickey • 460
0
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1
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326
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... Thanks, Aaron. Very helpful (as always).
...
written 12 months ago by
Peter Hickey • 460
2
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1
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326
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1
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... 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 ...
written 12 months ago by
Peter Hickey • 460
• updated
12 months ago by
Aaron Lun • 25k
Latest awards to Peter Hickey
Scholar
12 months ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
Supporter
12 months ago,
voted at least 25 times.
Popular Question
12 months ago,
created a question with more than 1,000 views.
For VariantAnnotation::readVcf is reordering the FORMAT field of my VCF file
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 VariantAnnotation::readVcf is reordering the FORMAT field of my VCF file
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges
Teacher
2.3 years ago,
created an answer with at least 3 up-votes.
For A: Error when generate mapToGenome
Scholar
2.3 years ago,
created an answer that has been accepted.
For A: About methylation data processing
Scholar
2.3 years ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
Popular Question
2.3 years 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
2.4 years ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
Scholar
3.7 years ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
Scholar
3.7 years ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
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