Showing : genomeIntervals • reset
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
12 months ago gshweta95 • 0
2
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3
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1.7k
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GRanges object from gene list
granges bed genomicranges genomeintervals deseq2
7.2 years ago rbronste ▴ 60
2
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1
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1.9k
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Extracting UTRs from exon and CDS data
genomeintervals UTRs exons CDS GenomicRanges
updated 7.7 years ago by ★ 11k • written 7.7 years ago by ▴ 110
3
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2
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What is the main difference between nclist and intervaltree algorithm in GenomicRanges packages ?
nclist genomeintervals
updated 9.2 years ago by 16k • written 9.2 years ago by ▴ 80
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1.4k
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cannot load genomeIntervals package
genomeIntervals
updated 9.8 years ago by ▴ 320 • written 10.0 years ago by • 0
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8
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2.0k
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Bug: readGff3 isRightOpen should be FALSE
genomeintervals
updated 9.8 years ago by ▴ 320 • written 9.8 years ago by • 0
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2.8k
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biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene") fails
BSgenome hexbin BSgenome IRanges genomeIntervals GenomicRanges girafe Rsamtools HiTC HiTC
updated 12.1 years ago by ★ 8.2k • written 12.1 years ago by ▴ 100
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convert "Genome_intervals_stranded" to "Genome_intervals"? (girafe)
Annotation convert genomeIntervals Annotation convert genomeIntervals
13.1 years ago delhomme@embl.de ★ 1.2k
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gff files: how to tell if right-open interval convention used?
genomeIntervals genomeIntervals
updated 14.0 years ago by 16k • written 14.0 years ago by ▴ 50
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stranded findOverlaps
Sequencing Annotation GO rtracklayer IRanges genomeIntervals Sequencing Annotation GO
15.2 years ago Robert Castelo ★ 3.4k
10 results • Page 1 of 1
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Answer: Model performance for spline modelling of RNA-seq timecourses in edgeR by Gordon Smyth 52k
I don't understand your question, because there is no difference between limma or glmFit or glmQLFit in terms of spline modeling or the tes…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…
Answer: DESeq2 - am I extracting results incorrectly? by James W. MacDonald 68k
If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…
Answer: Origin of the labels for the SingleCellMultiModal dataset by ATpoint ★ 4.8k
If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…
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Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Answer: SingleR with multiple single cell references
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