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 10.9 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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ORF lengths using Yeast Annotation package
yeast genomicranges
11.0 years ago dktarathym • 0
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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
11.1 years ago Dan Tenenbaum ★ 8.2k
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Complete variant toolbox: gmapR/VariantTools/VariantAnnotation - revived
VariantAnnotation Annotation GenomicRanges VariantAnnotation GenomicAlignments Annotation
11.2 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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994
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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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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
11.8 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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2.7k
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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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1.3k
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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 12.0 years ago by ★ 11k • written 12.0 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 12.0 years ago by ★ 11k • written 12.0 years ago by ▴ 760
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3
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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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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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810
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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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957
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Bioconductor refLocs2TranscriptLocs function
VariantAnnotation convert GenomicRanges VariantAnnotation VariantAnnotation convert
12.1 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 12.1 years ago by ★ 1.6k • written 12.1 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 12.2 years ago by ★ 4.2k • written 12.2 years ago by ★ 11k
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回复: Re: fRMA package
affxparser frma GenomicRanges affxparser frma GenomicRanges
12.2 years ago Hanyine ▴ 30
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1.6k
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FW: fRMA package
affxparser frma GenomicRanges affxparser frma GenomicRanges
12.2 years ago Li Liu ▴ 100
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4
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2.1k
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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
views
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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0
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923
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Semantics of GenomicRanges gaps()
GenomicRanges GenomicRanges
12.4 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
12.4 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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0
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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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3.2k
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brief quesion on DESeq2
Clustering GenomicRanges DESeq2 Clustering GenomicRanges DESeq2
updated 12.5 years ago by ▴ 20 • written 12.5 years ago by 43k
403 results • Page 7 of 9
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Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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