Showing : genomeIntervals • reset
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
8 months ago gshweta95 • 0
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GRanges object from gene list
granges bed genomicranges genomeintervals deseq2
6.8 years ago rbronste ▴ 60
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1.8k
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Extracting UTRs from exon and CDS data
genomeintervals UTRs exons CDS GenomicRanges
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ▴ 110
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What is the main difference between nclist and intervaltree algorithm in GenomicRanges packages ?
nclist genomeintervals
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 80
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1.3k
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cannot load genomeIntervals package
genomeIntervals
updated 9.4 years ago by ▴ 320 • written 9.7 years ago by • 0
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1.9k
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Bug: readGff3 isRightOpen should be FALSE
genomeintervals
updated 9.4 years ago by ▴ 320 • written 9.4 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 11.7 years ago by ★ 8.2k • written 11.7 years ago by ▴ 100
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convert "Genome_intervals_stranded" to "Genome_intervals"? (girafe)
Annotation convert genomeIntervals Annotation convert genomeIntervals
12.7 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 13.7 years ago by 16k • written 13.7 years ago by ▴ 50
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stranded findOverlaps
Sequencing Annotation GO rtracklayer IRanges genomeIntervals Sequencing Annotation GO
14.8 years ago Robert Castelo ★ 3.4k
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Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0
The updated version worked well on my data. Thank you!
Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di by James W. MacDonald 67k
The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…
Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k
Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…
Comment: Identifying potentially associated gene set to drug response using GSVA by Kent • 0
Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification by James W. MacDonald 67k
You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…
Votes
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
A: TopGO: How to retrieve the gene list related to a GO ID ?
A: Error in DESeqDataSet : some values in assay are not integers
A: correcting the batch effects in Limma and SVA
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