Showing : genomeintervals • reset
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
21 months ago gshweta95 • 0
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3
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1.9k
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GRanges object from gene list
granges bed genomicranges genomeintervals deseq2
8.0 years ago rbronste ▴ 60
2
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2.1k
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Extracting UTRs from exon and CDS data
genomeintervals UTRs exons CDS GenomicRanges
updated 8.4 years ago by ★ 11k • written 8.4 years ago by ▴ 110
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What is the main difference between nclist and intervaltree algorithm in GenomicRanges packages ?
nclist genomeintervals
updated 9.9 years ago by 16k • written 9.9 years ago by ▴ 80
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1.5k
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cannot load genomeIntervals package
genomeIntervals
updated 10.5 years ago by ▴ 320 • written 10.8 years ago by • 0
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8
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2.4k
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Bug: readGff3 isRightOpen should be FALSE
genomeintervals
updated 10.5 years ago by ▴ 320 • written 10.6 years ago by • 0
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3.0k
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biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene") fails
BSgenome hexbin BSgenome IRanges genomeIntervals GenomicRanges girafe Rsamtools HiTC HiTC
updated 12.8 years ago by ★ 8.2k • written 12.8 years ago by ▴ 100
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convert "Genome_intervals_stranded" to "Genome_intervals"? (girafe)
Annotation convert genomeIntervals Annotation convert genomeIntervals
13.9 years ago delhomme@embl.de ★ 1.2k
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1.3k
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gff files: how to tell if right-open interval convention used?
genomeIntervals genomeIntervals
updated 14.8 years ago by 16k • written 14.8 years ago by ▴ 50
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stranded findOverlaps
Sequencing Annotation GO rtracklayer IRanges genomeIntervals Sequencing Annotation GO
15.9 years ago Robert Castelo ★ 3.4k
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Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub? by jwp48 • 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond by Ludwig Geistlinger ▴ 80
When referring to the OSCA book including individual sub-books please cite the OSCA paper: Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
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Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
limma moderated t-statistics and B-statistics
A: how to control age and gender effect in expression data using DESeq2
how to control age and gender effect in expression data using DESeq2
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