Showing : genomeintervals • reset
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
20 months ago gshweta95 • 0
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GRanges object from gene list
granges bed genomicranges genomeintervals deseq2
7.9 years ago rbronste ▴ 60
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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 10.7 years ago by • 0
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2.3k
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Bug: readGff3 isRightOpen should be FALSE
genomeintervals
updated 10.5 years ago by ▴ 320 • written 10.5 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
13.8 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 14.7 years ago by 16k • written 14.7 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
10 results • Page 1 of 1
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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