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3
votes
3
replies
656
views
RSS for new packages unavailable?
RSS
4.4 years ago Malcolm Cook ★ 1.6k
0
votes
5
replies
2.2k
views
Yeast org.Sc.sgd.db lacks SYMBOL - should it have one? - how to make it interoperate with clusterProfiler in its absence?
annotation go clusterProfiler org.Sc.sgd.db
5.2 years ago Malcolm Cook ★ 1.6k
0
votes
5
replies
934
views
GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
genomicfeatures bug
updated 5.5 years ago by 65k • written 5.5 years ago by ★ 1.6k
0
votes
0
replies
958
views
coercion to Granges from empty data.frame ==> unexpected behavior ??
granges coercion
6.3 years ago Malcolm Cook ★ 1.6k
0
votes
0
replies
885
views
HowTo: install just html help on top of existing packages
bioclite package installation update
7.2 years ago Malcolm Cook ★ 1.6k
0
votes
1
reply
1.2k
views
HowTo? Provide a different fill color for each rectangle in an Gviz AnnotationTrack ?
Gviz color
updated 7.8 years ago by ★ 1.6k • written 7.8 years ago by ★ 1.6k
3
votes
3
replies
1.5k
views
Using a single R installation with multiple BioConductor library installations - opinions & best practices sought
version release library
updated 9.2 years ago by ▴ 400 • written 9.2 years ago by ★ 1.6k
7
votes
5
replies
4.1k
views
Is Bioconductor 3.0 compatible with R 3.1.2?
version compatibility
updated 9.5 years ago by ▴ 220 • written 9.5 years ago by ★ 1.6k
0
votes
2
replies
1.0k
views
IRanges::Rle::[ arguably should return NA when i is out of range
updated 10.2 years ago by 16k • written 10.2 years ago by ★ 1.6k
0
votes
1
reply
360
views
IRanges/List oddity: do.call of `c` on a list of IRangesList returns
updated 10.2 years ago by 16k • written 10.3 years ago by ★ 1.6k
0
votes
2
replies
1.8k
views
subsetting SummarizedExperiments - a proposal (or a hack?)
Cancer IRanges GenomicRanges PROMISE Cancer IRanges GenomicRanges PROMISE
updated 10.3 years ago by ★ 13k • written 10.3 years ago by ★ 1.6k
0
votes
7
replies
1.7k
views
subsetting SummarizedExperiments - a proposal (or a hack?)
updated 10.3 years ago by 25k • written 10.3 years ago by ★ 1.6k
0
votes
0
replies
670
views
summarizeOverlaps colData does NOT contain countBam() summary data
10.3 years ago Malcolm Cook ★ 1.6k
0
votes
1
reply
394
views
error in "count" for SummarizedExperiment in easyRNASeq
updated 10.4 years ago by ▴ 320 • written 10.4 years ago by ★ 1.6k
0
votes
2
replies
1.7k
views
autoplot transcriptDb error with some regions
TranscriptDb biovizBase ggbio TranscriptDb biovizBase ggbio
updated 10.5 years ago by ▴ 490 • written 10.5 years ago by ★ 1.6k
0
votes
1
reply
704
views
BUG: median(IRanges::Rle(NA), na.rm=TRUE)) should return NA
updated 10.7 years ago by 16k • written 10.7 years ago by ★ 1.6k
0
votes
0
replies
620
views
BUG: median(IRanges::Rle(NA),na.rm=TRUE)) should return NA
10.7 years ago Malcolm Cook ★ 1.6k
0
votes
3
replies
1.1k
views
BUG? when setting mcols of a GRanges to a DataFrame one of whose columns is an ordered factor
updated 10.8 years ago by 16k • written 10.8 years ago by ★ 1.6k
0
votes
2
replies
1.5k
views
GViz - successes and a few hopes
annotate Gviz annotate Gviz
updated 10.8 years ago by ★ 1.6k • written 10.8 years ago by ★ 1.6k
0
votes
3
replies
1.0k
views
ggbio facet_gr example sought
updated 10.8 years ago by ★ 11k • written 10.8 years ago by ★ 1.6k
0
votes
5
replies
1.3k
views
[Rd] enabling reproducible research & R package management & install.package.version & BiocLite
GO GO
11.2 years ago Malcolm Cook ★ 1.6k
0
votes
5
replies
1.7k
views
enabling reproducible research & R package management & install.package.version & BiocLite
updated 11.2 years ago by ▴ 170 • written 11.2 years ago by ★ 1.6k
0
votes
0
replies
2.0k
views
emacs org mode html export using jQuery DataTables (WAS: new package for generating interactive HTML reports)
Network limma GOstats GSEAlm edgeR ReportingTools Network limma GOstats GSEAlm edgeR
11.4 years ago Malcolm Cook ★ 1.6k
0
votes
0
replies
536
views
IRanges/List oddity: do.call of `c` on a list of IRangesList returns "list" only when the list is named
11.5 years ago Malcolm Cook ★ 1.6k
0
votes
0
replies
658
views
[Bioc-devel] knowing what is changed/new in release patches
IRanges IRanges
11.5 years ago Malcolm Cook ★ 1.6k
0
votes
4
replies
730
views
knowing what is changed/new in release patches
IRanges IRanges
updated 11.5 years ago by ★ 6.5k • written 11.5 years ago by ★ 1.6k
0
votes
4
replies
732
views
multicore and GRangesList [Resurrected]
updated 11.7 years ago by 25k • written 11.7 years ago by ★ 1.6k
0
votes
2
replies
647
views
transcriptLocs2refLocs Bug when strand is negative
updated 11.7 years ago by 25k • written 11.7 years ago by ★ 1.6k
0
votes
4
replies
853
views
BUG in Genomic(Features|Ranges): names(unlist(transcriptsBy(txdb, 'gene'))) is UNRELIABLE!!!
GenomicRanges GenomicRanges
updated 11.7 years ago by 25k • written 11.7 years ago by ★ 1.6k
0
votes
0
replies
1.3k
views
[Engineers for ensemblgenomes.org #251937] BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info …
Drosophila melanogaster TranscriptDb biomaRt GenomicFeatures genomes Drosophila melanogaster
11.9 years ago Malcolm Cook ★ 1.6k
0
votes
3
replies
1.1k
views
rtracklayer proposal for ISSUE: import.gff3 asRangedData=FALSE fails when strand is '.'
updated 12.1 years ago by 16k • written 12.1 years ago by ★ 1.6k
0
votes
0
replies
1.3k
views
[Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred f…
Cancer Organism biomaRt genomes Cancer Organism biomaRt genomes
12.1 years ago Malcolm Cook ★ 1.6k
0
votes
3
replies
1.0k
views
[Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred f…
Cancer Organism biomaRt GenomicFeatures Cancer Organism biomaRt GenomicFeatures
updated 12.3 years ago by ▴ 660 • written 12.3 years ago by ★ 1.6k
0
votes
0
replies
1.3k
views
BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute fr…
TranscriptDb biomaRt GenomicFeatures TranscriptDb biomaRt GenomicFeatures
12.3 years ago Malcolm Cook ★ 1.6k
0
votes
3
replies
1.7k
views
GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR i…
biomaRt biomaRt
updated 12.3 years ago by ▴ 660 • written 12.3 years ago by ★ 1.6k
0
votes
1
reply
1.1k
views
error "Too many pushAbortHandlers, can only handle 11" while exporting bedGraph/bigWig using rtracklayer from Bioconductor
rtracklayer rtracklayer
updated 12.3 years ago by ★ 11k • written 12.3 years ago by ★ 1.6k
0
votes
5
replies
1.3k
views
FW: GenomicFeatures::makeTranscriptDbFromBiomart - Error in callSuper(...) : could not find function "initRefFields"
biomaRt biomaRt
updated 12.3 years ago by ★ 7.2k • written 12.3 years ago by ★ 1.6k
0
votes
0
replies
1.1k
views
GenomicFeatures::makeTranscriptDbFromBiomart - Error in callSuper(...) : could not find function "initRefFields"
biomaRt biomaRt
12.3 years ago Malcolm Cook ★ 1.6k
0
votes
5
replies
1.3k
views
GenomicFeatures makeTranscriptDbFromBiomart failure
updated 12.4 years ago by 16k • written 12.4 years ago by ★ 1.6k
0
votes
2
replies
1.1k
views
biomaRt access to ensemble genomes 11 fungi_mart_11
genomes genomes
updated 12.4 years ago by ▴ 60 • written 12.4 years ago by ★ 1.6k
0
votes
3
replies
1.5k
views
HowTo: "Extract masked sequences" / "insert Ns for repeat masked regions"
GO BSgenome BSgenome GO BSgenome BSgenome
updated 12.7 years ago by 16k • written 12.7 years ago by ★ 1.6k
0
votes
5
replies
976
views
Re(surrecting): [Bioc-sig-seq] Rsamtools countBam labeling
updated 13.1 years ago by 25k • written 13.1 years ago by ★ 1.6k
0
votes
1
reply
849
views
Mapping genomic coordinates to transcript coordinates? (revived)
GenomicFeatures GenomicFeatures
updated 13.2 years ago by ▴ 90 • written 13.2 years ago by ★ 1.6k
0
votes
2
replies
1.6k
views
extending GenomicFeatures to makeTranscriptDbFrom other sources (i.e. GFF3)
TranscriptDb biomaRt TranscriptDb biomaRt
updated 13.2 years ago by ★ 7.2k • written 13.3 years ago by ★ 1.6k
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