Showing : genomicranges • reset
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rtracklayer importing gtf files
rtracklayer DESeq GenomicRanges rtracklayer DESeq GenomicRanges
updated 12.6 years ago by ★ 11k • written 12.6 years ago by ★ 13k
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Calculate Outer Positions of GappedAlignmentPairs
Coverage GenomicRanges Coverage GenomicRanges
updated 12.7 years ago by ★ 11k • written 12.7 years ago by ★ 1.6k
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[Solved] GRanges error - Error: identical(colnames(classinfo), colnames(out)) is not TRUE
GenomicRanges GenomicRanges
12.7 years ago Richard Birnie ▴ 10
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1
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1.6k
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Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Preprocessing BSgenome biomaRt BSgenome GenomicRanges MEDIPS Preprocessing BSgenome MEDIPS
updated 12.7 years ago by ▴ 570 • written 12.7 years ago by ▴ 290
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GRanges error - Error: identical(colnames(classinfo), colnames(out)) is not TRUE
GenomicRanges GenomicRanges
12.7 years ago Guest User ★ 13k
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1
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biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene") fails
BSgenome hexbin BSgenome IRanges genomeIntervals GenomicRanges girafe Rsamtools HiTC HiTC
updated 12.7 years ago by ★ 8.2k • written 12.7 years ago by ▴ 100
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pileup coverage from BAM file
Coverage Cancer IRanges GenomicRanges Coverage Cancer IRanges GenomicRanges
12.7 years ago Martin Morgan 25k
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2
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distanceToNearest in GenomicRanges
GenomicRanges GenomicRanges
updated 12.8 years ago by 68k • written 12.8 years ago by ▴ 60
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8
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3.0k
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Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges
GenomicRanges GenomicRanges
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ▴ 760
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3
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1.2k
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split(SE, seqnames(SE)) doesn't work anymore
GenomicRanges GenomicRanges
12.8 years ago Tim Triche ★ 4.2k
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4
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Using GenomicRanges with table data
IRanges GenomicRanges IRanges GenomicRanges
updated 12.9 years ago by ★ 13k • written 12.9 years ago by ▴ 60
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0
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get synthetic exon dataset with easyRNASeq
RNASeq Alignment Annotation Normalization GO PROcess GenomicRanges DEXSeq easyRNASeq GO
13.0 years ago delhomme@embl.de ★ 1.2k
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450K annotation: discrepancy between GEO GPL and Bioconductor annotation
Annotation db0 probe annotate PROcess GenomicFeatures GenomicRanges Annotation db0 probe
13.1 years ago Marc Carlson ★ 7.2k
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1
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1.2k
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interpretation & visualization methylation data (illum 450k)
GenomicRanges minfi GenomicRanges minfi
updated 13.1 years ago by ★ 6.5k • written 13.1 years ago by ★ 4.1k
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1
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1.1k
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warnings on easyRNASeq package
Annotation Organism PROcess GenomicRanges easyRNASeq Annotation Organism PROcess
updated 13.1 years ago by ▴ 10 • written 13.1 years ago by ★ 1.2k
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4
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BUG in Genomic(Features|Ranges): names(unlist(transcriptsBy(txdb, 'gene'))) is UNRELIABLE!!!
GenomicRanges GenomicRanges
updated 13.2 years ago by 25k • written 13.2 years ago by ★ 1.6k
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0
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GenomicRanges: nearest() for GRanges not returning overlaps
IRanges GenomicRanges IRanges GenomicRanges
13.3 years ago Valerie Obenchain ★ 6.8k
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1
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1.1k
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nearest for GRanges ignoring overlapping ranges
Cancer IRanges GenomicRanges Cancer IRanges GenomicRanges
updated 13.3 years ago by ★ 6.8k • written 13.3 years ago by ▴ 740
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2
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distanceToNearest for GRanges?
IRanges GenomicRanges IRanges GenomicRanges
updated 13.3 years ago by ★ 6.8k • written 13.3 years ago by ▴ 740
0
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4
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5.3k
views
GRanges DitancetoNearest query
Transcription GenomicRanges Transcription GenomicRanges
updated 13.3 years ago by ★ 13k • written 13.3 years ago by ▴ 150
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8
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2.5k
views
good news and bad news
Infrastructure Cancer IRanges GenomicRanges Infrastructure Cancer IRanges GenomicRanges
updated 13.3 years ago by ★ 13k • written 13.3 years ago by 16k
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0
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1.4k
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Problem with nearest() in GenomicRanges
GenomicRanges GenomicRanges
13.3 years ago Chris Whelan ▴ 60
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3
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1.6k
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Problem with nearest() in GenomicRanges
GenomicRanges GenomicRanges
updated 13.3 years ago by ★ 6.8k • written 13.3 years ago by ▴ 60
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5
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1.5k
views
GappedAlignmentPairs requests
Alignment Cancer GenomicRanges Alignment Cancer GenomicRanges
updated 13.4 years ago by ★ 11k • written 13.4 years ago by 16k
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2
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1.5k
views
Operations on GenomicRanges metadata information
Genetics GenomicRanges Genetics GenomicRanges
updated 13.4 years ago by ★ 11k • written 13.4 years ago by ▴ 80
0
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4
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1.4k
views
readGappedAlignmentPairs with multimapping reads
GenomicRanges GenomicRanges
updated 13.5 years ago by 16k • written 13.5 years ago by ★ 13k
0
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7
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1.7k
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distanceToNearest for GRanges?
Cancer GenomicRanges Cancer GenomicRanges
updated 13.6 years ago by ▴ 420 • written 13.6 years ago by ★ 6.8k
0
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2
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1.3k
views
curious IRanges error when sort()ing a GRanges
GO BSgenome BSgenome GenomicRanges GO BSgenome BSgenome GenomicRanges
updated 13.7 years ago by 16k • written 13.7 years ago by ★ 4.2k
0
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1
reply
1.2k
views
Installation errors for DESeq, Genomic Ranges etc.
rtracklayer DESeq GenomicRanges BiocInstaller rtracklayer DESeq GenomicRanges BiocInstaller
updated 13.8 years ago by 25k • written 13.8 years ago by ▴ 220
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1
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1.9k
views
GenomicRanges requires a IRanges version not available in the repository
GenomicRanges htSeqTools GenomicRanges htSeqTools
updated 13.8 years ago by 6.7k • written 13.8 years ago by ▴ 80
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3
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2.2k
views
RE : maping SNPs
SNP Annotation Cancer SNPlocs TranscriptDb GenomicFeatures GenomicRanges SNP Annotation
updated 13.8 years ago by 16k • written 13.8 years ago by ▴ 450
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0
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831
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narrow on GappedAlignments fails with error
Cancer GenomicRanges Cancer GenomicRanges
13.8 years ago Hervé Pagès 16k
0
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1
reply
1.2k
views
using ensembl archive in GenomicRanges
GenomicRanges GenomicRanges
updated 13.9 years ago by ▴ 970 • written 13.9 years ago by ▴ 270
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3
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1.5k
views
Some more rtracklayer questions (re: WIG and .VSTEP files)
Coverage rtracklayer GenomicRanges Coverage rtracklayer GenomicRanges
updated 14.0 years ago by ★ 11k • written 14.0 years ago by ★ 4.2k
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0
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940
views
countGenomicOverlaps output
GenomicRanges GenomicRanges
14.2 years ago Valerie Obenchain ★ 6.8k
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12
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3.1k
views
more stupid *Ranges questions...
Transcription ChIPpeakAnno GenomicRanges Transcription ChIPpeakAnno GenomicRanges
updated 14.2 years ago by ★ 11k • written 14.2 years ago by ★ 4.2k
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3
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1.1k
views
rtracklayer import.bed pipe inconsistency
rtracklayer GenomicRanges rtracklayer GenomicRanges
updated 14.2 years ago by ★ 11k • written 14.2 years ago by ▴ 20
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6
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1.7k
views
wishlist for readGappedAlignments
GenomicRanges Rsamtools GenomicRanges Rsamtools
updated 14.3 years ago by 25k • written 14.3 years ago by ▴ 420
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0
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3.3k
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unique, duplicated, order, etc... on a GRanges object
Cancer GenomicRanges Cancer GenomicRanges
14.3 years ago Hervé Pagès 16k
0
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1
reply
1.5k
views
help needed in namespace definition
GenomicRanges PICS GenomicRanges PICS
updated 14.3 years ago by 16k • written 14.3 years ago by ▴ 10
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7
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2.3k
views
Probe ID to Sequence
SNPlocs GenomicRanges SNPlocs GenomicRanges
updated 14.3 years ago by ★ 4.2k • written 14.3 years ago by ▴ 400
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1
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1.2k
views
RMAPPER and whole genome TFBS information
RMAPPER GenomicRanges RMAPPER GenomicRanges
updated 14.6 years ago by 6.7k • written 14.6 years ago by ▴ 140
0
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1
reply
798
views
GenomicRangesUseCases Manual :: Typo?
GenomicRanges GenomicRanges
updated 14.6 years ago by ★ 7.2k • written 14.6 years ago by ▴ 20
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2
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1.3k
views
Problem loading saved GenomicRanges object
GenomicRanges GenomicRanges
updated 14.8 years ago by 6.7k • written 14.8 years ago by ▴ 550
0
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2
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988
views
bug report for GenomicRanges::findOverlaps
GenomicRanges GenomicRanges
updated 14.9 years ago by 16k • written 14.9 years ago by ★ 6.5k
0
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7
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2.4k
views
multicore and GRangesList
GenomicRanges GenomicRanges
updated 14.9 years ago by 25k • written 14.9 years ago by ▴ 200
0
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0
replies
981
views
findOverlaps for GRanges
IRanges GenomicRanges IRanges GenomicRanges
15.1 years ago Kasper Daniel Hansen ★ 6.5k
0
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0
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1.3k
views
Flagging overlapping gene exons (was Re: Question about CSAMA10 ...)
Annotation Cancer IRanges GenomicFeatures GenomicRanges Annotation Cancer IRanges
15.2 years ago Steve Lianoglou ★ 13k
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2
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1.5k
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GenomicRanges countOverlaps error
Cancer GenomicRanges Cancer GenomicRanges
updated 15.2 years ago by ★ 13k • written 15.2 years ago by ▴ 20
0
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4
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1.5k
views
Error mapping RNA-seq data to genome
GenomicFeatures GenomicRanges GenomicFeatures GenomicRanges
updated 15.3 years ago by 25k • written 15.3 years ago by ★ 1.3k
403 results • Page 8 of 9
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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