Admin: Hervé Pagès
Hervé Pagès ♦♦ 12k
- Reputation:
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- 11 years, 6 months ago
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Posts by Hervé Pagès
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59
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... Hi Michael,
FWIW, you could double-confirm your results by counting again with summarizeOverlaps() from the GenomicAlignments package. If your data is "reversely stranded", then invert the read strand with invertStrand(reads) before passing them to summarizeOverlaps(). Alternatively, if the reads a ...
written 7 days ago by
Hervé Pagès ♦♦ 12k
0
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69
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1
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... Excellent! Thanks. H.
...
written 13 days ago by
Hervé Pagès ♦♦ 12k
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1
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69
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... Hi Martin,
I was wondering if there is a way to avoid that upfront division of the job i.e. have bplapply() work asynchronously (like bpiterate()) where the n workers receive only 1 element of the list at a time. Can this be controlled via the BPPARAM argument or should I use bpiterate() for that? ...
written 13 days ago by
Hervé Pagès ♦♦ 12k
0
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2
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57
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Answer:
A: DNAString - Long String
... The max length of a DNAString object is .Machine$integer.max, that is 2^31-1 on any platform I know.
H.
...
written 14 days ago by
Hervé Pagès ♦♦ 12k
0
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48
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... Hi Matt,
Thanks for the report. I made those changes in GenomicFeatures 1.28.3 (release) and 1.29.6 (devel).
H.
...
written 14 days ago by
Hervé Pagès ♦♦ 12k
0
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51
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... Hi Matt,
Note that the default behavior of the seqlevels setter has not changed (has been raising an error if the object needs pruning since the beginning).
I generally try my best to make this kind of changes smoother, typically by using deprecation warnings. I'm not too keen on the idea of using ...
written 21 days ago by
Hervé Pagès ♦♦ 12k
0
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185
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... Hi Matt,
Thanks for keeping a diligent eye on this :-) Should be fixed in GenomicFeatures 1.28.2 (release) and 1.29.5 (devel). Please allow again between 24h and 48h for these new versions to become available via biocLite().
H.
...
written 22 days ago by
Hervé Pagès ♦♦ 12k
0
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68
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1
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... This is fixed in GenomeInfoDb 1.12.1. People running the current version of Bioconductor (i.e. BioC 3.5) can update their installation with biocLite().
It seems that the OP is running BioC 3.4, which is not current. Note that we don't provide fixes for old Bioconductor versions. "The fix" is to upg ...
written 22 days ago by
Hervé Pagès ♦♦ 12k
0
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1
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80
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1
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... This is now fixed in Biostrings 2.44.1. With this new version:
library(Biostrings)
getGeneticCode("11")
# TTT TTC TTA TTG TCT TCC TCA TCG TAT TAC TAA TAG TGT TGC TGA TGG CTT
# "F" "F" "L" "L" "S" "S" "S" "S" "Y" "Y" "*" "*" "C" "C" "*" "W" "L"
# CTC CTA CTG CCT CCC CCA CCG CAT CAC CAA CAG CGT CG ...
written 22 days ago by
Hervé Pagès ♦♦ 12k
0
votes
1
answers
49
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1
answers
... Hi Charles,
FWIW the DelayedArray package allows you to manipulate a DataFrame of Rle columns as a matrix-like object by just wrapping it inside a DelayedArray object (you do this by calling DelayedArray() on it). See ?DelayedArray for more information. After applying (delayed) operations on it, yo ...
written 23 days ago by
Hervé Pagès ♦♦ 12k
Latest awards to Hervé Pagès
Teacher
4 days ago,
created an answer with at least 3 up-votes.
For A: How do I merge a list of GRanges?
Scholar
17 days ago,
created an answer that has been accepted.
For A: Extracting Coordinates of startcodon from Grangeslist
Scholar
24 days ago,
created an answer that has been accepted.
For A: Extracting Coordinates of startcodon from Grangeslist
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: A bug of "seqlevels<-" on TxDb
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: A bug of "seqlevels<-" on TxDb
Scholar
8 weeks ago,
created an answer that has been accepted.
For A: A bug of "seqlevels<-" on TxDb
Supporter
8 weeks ago,
voted at least 25 times.
Teacher
9 weeks ago,
created an answer with at least 3 up-votes.
For A: How do I merge a list of GRanges?
Scholar
9 weeks ago,
created an answer that has been accepted.
For A: A bug of "seqlevels<-" on TxDb
Commentator
11 weeks ago,
created a comment with at least 3 up-votes.
For C: Error in GRanges: could not find symbol "recursive" in environment of the generi
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: How do I merge a list of GRanges?
Scholar
3 months ago,
created an answer that has been accepted.
For A: A bug of "seqlevels<-" on TxDb
Scholar
4 months ago,
created an answer that has been accepted.
For A: A bug of "seqlevels<-" on TxDb
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: XStringSet operations discard names - how to address?
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: kmer and zscore calculation
Scholar
14 months ago,
created an answer that has been accepted.
For A: XStringSet operations discard names - how to address?
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: pairwiseAlignments coordinate mapping?
Scholar
14 months ago,
created an answer that has been accepted.
For A: pairwiseAlignments coordinate mapping?
Scholar
14 months ago,
created an answer that has been accepted.
For A: vcountPattern for Pattern Contained within or Containing Subject
Scholar
14 months ago,
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For A: how much positions overlapped for each pair of the pairs obtained by findover
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: makeTxDbFromUCSC fails to download refLink table
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: overlapsAny for elements in GRangesList
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