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
7.9 years ago rbronste ▴ 60
2
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1
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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 10.7 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 10.5 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
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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…
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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