Showing : Genomicranges • reset
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Get exonFrames metadata from makeTranscriptDbFromUCSC command
genomicfeatures genomicranges ucsc
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 90
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2
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Combine two GRanges to a single GRangesList
granges grangeslist GenomicRanges
updated 10.8 years ago by 25k • written 10.8 years ago by 21k
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updateObject() fails for old serialized GRanges objects
genomicranges
updated 10.8 years ago by 16k • written 10.9 years ago by ▴ 90
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1
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findOverlaps error with Gviz
gviz genomicranges software error
updated 10.9 years ago by ★ 1.6k • written 10.9 years ago by ▴ 40
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4
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devel version: rtracklayer depends on GenomicRanges 1.19.3 but that's not available
rtracklayer genomicranges bioclite
updated 10.9 years ago by ★ 7.2k • written 10.9 years ago by ▴ 740
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10
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mapCoords for converting genomic coordinates to cDNA coordinates?
genomicranges
updated 10.9 years ago by ★ 6.8k • written 10.9 years ago by ▴ 10
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4
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ORF lengths using Yeast Annotation package
yeast genomicranges
10.9 years ago dktarathym • 0
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1.6k
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Error running table() on an RleList returned by coverage()
GenomicRanges S4Vectors
updated 11.0 years ago by 16k • written 11.0 years ago by ★ 5.2k
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[Bioc-devel] AnnotatioDbi Biostrings load order breaks GenomicFiles summary method
GO Biostrings rtracklayer GenomicRanges BiocParallel GenomicFiles
11.0 years ago Dan Tenenbaum ★ 8.2k
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Complete variant toolbox: gmapR/VariantTools/VariantAnnotation - revived
VariantAnnotation Annotation GenomicRanges VariantAnnotation GenomicAlignments Annotation
11.1 years ago Valerie Obenchain ★ 6.8k
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Complete variant toolbox: gmapR/VariantTools/VariantAnnotation - revived
VariantAnnotation GenomicRanges VariantAnnotation VariantAnnotation GenomicRanges
updated 11.2 years ago by ★ 3.4k • written 11.2 years ago by ★ 6.8k
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[Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...
Cancer GenomicRanges Cancer GenomicRanges
updated 11.2 years ago by ★ 1.3k • written 11.2 years ago by 16k
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1
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Installation issue with package GenomicRanges_1.17.18.tar.gz
GenomicRanges GenomicRanges
updated 11.3 years ago by ★ 13k • written 11.3 years ago by ▴ 10
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4
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GenomicRanges select parameter
GenomicRanges ASSIGN GenomicRanges ASSIGN
updated 11.3 years ago by ▴ 30 • written 11.3 years ago by ★ 11k
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3
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Use of non-exported `clone` function from GenomicRange package
GenomicRanges GenomicRanges
updated 11.5 years ago by ★ 11k • written 11.5 years ago by ▴ 760
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2
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subsetting SummarizedExperiments - a proposal (or a hack?)
Cancer IRanges GenomicRanges PROMISE Cancer IRanges GenomicRanges PROMISE
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ★ 1.6k
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1.0k
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Most efficient way to compute width of overlap of multiple features
GenomicRanges GenomicRanges
updated 11.7 years ago by ★ 11k • written 11.7 years ago by ▴ 290
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genomicRanges/Features reads counted in features and inbetween features is not the total number of counted reads
GenomicRanges GenomicRanges
11.7 years ago Sam McInturf ▴ 300
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1.7k
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easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges Rsubread easyRNASeq GO
updated 11.8 years ago by ▴ 320 • written 11.8 years ago by 53k
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easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
11.8 years ago Nicolas Delhomme ▴ 320
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2.6k
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VariantTools installation problem: dependencies not available
IRanges GenomicRanges VariantTools XVector IRanges GenomicRanges VariantTools XVector
updated 11.9 years ago by ★ 11k • written 11.9 years ago by ▴ 360
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2
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Bug in GenomicRanges 1.14.3, as(from, "GRanges") not working for RleViewsList
GenomicRanges GenomicRanges
updated 11.9 years ago by 16k • written 11.9 years ago by ▴ 20
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Problem with GenomicRanges 1.14.3, as(from, \"GRanges\") not working for RleViewsList
GenomicRanges GenomicRanges
11.9 years ago Guest User ★ 13k
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3
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1.2k
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VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'
GenomicRanges GenomicRanges
updated 11.9 years ago by ★ 11k • written 11.9 years ago by ★ 1.3k
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2
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how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 11.9 years ago by ★ 11k • written 11.9 years ago by 16k
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4
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Getting first or last hit from a Hits object
IRanges GenomicRanges IRanges GenomicRanges
updated 11.9 years ago by ★ 11k • written 11.9 years ago by ▴ 760
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Bioconductor refLocs2TranscriptLocs function
VariantAnnotation convert GenomicRanges VariantAnnotation VariantAnnotation convert
12.0 years ago Michael Lawrence ★ 11k
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5
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2.1k
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Fwd: summarizeOverlaps behavior on RNA-Seq paired end stranded data
GenomicRanges GenomicRanges
updated 12.0 years ago by ★ 6.8k • written 12.0 years ago by ▴ 160
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summarizeOverlaps behavior on RNA-Seq paired end stranded data
GenomicRanges GenomicRanges
12.0 years ago Abhishek Pratap ▴ 10
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0
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807
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VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'
GenomicRanges GenomicRanges
12.0 years ago Valerie Obenchain ★ 6.8k
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1
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1.8k
views
Lifting over a bam file with Rsamtools and GenomicRanges
GenomicRanges genomes GenomicRanges genomes
updated 12.0 years ago by ★ 11k • written 12.0 years ago by ★ 13k
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0
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953
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Bioconductor refLocs2TranscriptLocs function
VariantAnnotation convert GenomicRanges VariantAnnotation VariantAnnotation convert
12.0 years ago Michael Lawrence ★ 11k
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4
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2.3k
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bug in GenomicRanges gaps?
GenomicFeatures GenomicRanges GenomicFeatures GenomicRanges
updated 12.0 years ago by ★ 1.6k • written 12.0 years ago by ▴ 220
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5
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Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 12.1 years ago by ★ 6.8k • written 12.1 years ago by ▴ 300
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Course: Understanding R / Bioconductor, Sept 30-Oct 1, Seattle
Cancer Biostrings biomaRt IRanges GenomicRanges Cancer Biostrings biomaRt IRanges
12.1 years ago Martin Morgan 25k
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2.5k
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Semantics of GenomicRanges gaps()
Cancer GenomicRanges trigger Cancer GenomicRanges trigger
updated 12.1 years ago by ★ 6.8k • written 12.1 years ago by ▴ 210
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2
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*Ranges paper published
Infrastructure IRanges GenomicFeatures GenomicRanges Infrastructure IRanges GenomicFeatures
updated 12.1 years ago by ★ 4.2k • written 12.1 years ago by ★ 11k
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回复: Re: fRMA package
affxparser frma GenomicRanges affxparser frma GenomicRanges
12.1 years ago Hanyine ▴ 30
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1.6k
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FW: fRMA package
affxparser frma GenomicRanges affxparser frma GenomicRanges
12.1 years ago Li Liu ▴ 100
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4
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about GenomicRanges keepseqlevel deprecation and ggbio
GenomicRanges ggbio GenomicRanges ggbio
updated 12.2 years ago by ★ 11k • written 12.2 years ago by ▴ 90
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9
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ReportingTools - trouble incorporating annotations
Annotation edgeR GenomicRanges Annotation edgeR GenomicRanges
updated 12.3 years ago by 68k • written 12.3 years ago by ▴ 300
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3
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2.4k
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diffbind, paired end reads
GenomicRanges DiffBind GenomicRanges DiffBind
updated 12.3 years ago by ▴ 670 • written 12.3 years ago by ★ 5.2k
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0
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1.7k
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return value used for filter amongst attributes, getBM(), biomaRt
GO biomaRt GenomicRanges GO biomaRt GenomicRanges
12.3 years ago James Perkins ▴ 120
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9
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2.7k
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using a gtf file to map reads
GenomicRanges DESeq2 GenomicRanges DESeq2
updated 12.3 years ago by ★ 11k • written 12.3 years ago by ▴ 300
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1
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1.1k
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Semantics of GenomicRanges gaps()
Cancer GenomicRanges Cancer GenomicRanges
updated 12.3 years ago by ★ 11k • written 12.3 years ago by 16k
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920
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Semantics of GenomicRanges gaps()
GenomicRanges GenomicRanges
12.3 years ago Alex Gutteridge ▴ 650
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0
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1.2k
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[devteam-bioc] sort error in GRange
rtracklayer GenomicRanges rtracklayer GenomicRanges
12.3 years ago Valerie Obenchain ★ 6.8k
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1
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1.4k
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summarizeOverlaps mode ignoring inter feature overlaps
GenomicRanges Rsamtools GenomicRanges Rsamtools
updated 12.4 years ago by ★ 1.7k • written 12.4 years ago by ★ 6.8k
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1.1k
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sort error in GRange
GenomicRanges GenomicRanges
12.4 years ago Guest User ★ 13k
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5
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3.1k
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brief quesion on DESeq2
Clustering GenomicRanges DESeq2 Clustering GenomicRanges DESeq2
updated 12.4 years ago by ▴ 20 • written 12.5 years ago by 43k
403 results • Page 7 of 9
Recent ...
Replies
Answer: replace cat with message in glmTreat when lfc = 0 by Gordon Smyth 53k
Yes, I agree that the message should be a `message` rather than `cat` output, and the message is perhaps not needed at all, because anyone …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
How did you make this plot? I've never seen an MDS plot from limma/edgeR with axis scale going from -200 to 200. Personally, I would go ah…
Comment: readDNAStringSet with non DNA characters by biomiha ▴ 20
DECIPHER does the trick, thank you!
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by James W. MacDonald 68k
It may not be that common for bulk RNA-Seq, but in my experience it's very common for bulk miRNA-Seq.
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Nice. That's great to hear. `sva` was actually the next step I was planning to try. My colleagues haven't seen this kind of pattern before …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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