Showing : GenomicRanges • reset
0
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4
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1.6k
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Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 6.5 years ago by 16k • written 6.5 years ago by ▴ 10
3
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4
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1.6k
views
ORF lengths using Yeast Annotation package
yeast genomicranges
9.5 years ago dktarathym • 0
5
votes
10
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3.1k
views
tileGenome for overlapping ranges?
genomicranges
updated 8.7 years ago by • 0 • written 9.2 years ago by ▴ 740
1
vote
14
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1.9k
views
DistanceToNearest() error: 'nLnode' and 'nRnode' must be single integers
genomicranges DistanceToNearest
updated 7.6 years ago by ★ 6.8k • written 7.6 years ago by ▴ 20
1
vote
11
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2.4k
views
Had to remove duplicated() in order to install GenomicRanges 1.22 on top of 1.20 on linux
installation genomicranges summarizedexperiment
8.5 years ago • updated 8.4 years ago knb • 0
0
votes
7
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1.8k
views
multicore and GRangesList
GenomicRanges GenomicRanges
updated 13.3 years ago by 25k • written 13.3 years ago by ▴ 200
5
votes
8
replies
2.2k
views
closest-features equivalent in Bioconductor for finding closest gene(s)
genomicranges granges iranges annotatepeak
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ▴ 80
0
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4
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1.1k
views
readGappedAlignmentPairs with multimapping reads
GenomicRanges GenomicRanges
updated 11.9 years ago by 16k • written 11.9 years ago by ★ 13k
0
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4
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1.8k
views
Getting first or last hit from a Hits object
IRanges GenomicRanges IRanges GenomicRanges
updated 10.5 years ago by ★ 11k • written 10.5 years ago by ▴ 740
17
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4
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16k
views
How to properly sort GRanges?
granges genomicranges sort seqnames order
updated 9.0 years ago by ▴ 30 • written 9.4 years ago by ▴ 660
5
votes
8
replies
8.7k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 2.2 years ago by • 0 • written 8.6 years ago by ▴ 50
2
votes
3
replies
1.2k
views
Split Genomic Ranges With Reference Overlaps (Centromere)
granges genomicranges split
written 7.0 years ago by • 0
6
votes
12
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1.8k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
5.2 years ago foehn ▴ 100
0
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6
replies
3.2k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster quasR genomicfeatures genomicranges alignment
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 70
6
votes
4
replies
1.3k
views
Aggregate read counts by non-uniform overlapping sliding windows
granges genomicranges featurecounts
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ▴ 20
0
votes
3
replies
962
views
Bioconductor refLocs2TranscriptLocs function
VariantAnnotation convert GenomicRanges VariantAnnotation VariantAnnotation convert
10.6 years ago Michael Lawrence ★ 11k
3
votes
10
replies
6.8k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
4.8 years ago Robert ▴ 10
11
votes
13
replies
4.0k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
3.4 years ago • updated 3.2 years ago rohitsatyam102 ▴ 20
8
votes
9
replies
6.0k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 8.8 years ago by • 0 • written 8.8 years ago by ★ 1.5k
3
votes
2
replies
1.1k
views
Match all DNAString Occurences in a BSgenome
bsgenome genomicranges function creation
7.7 years ago ewjwallace ▴ 10
3
votes
4
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2.0k
views
ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds
chipseeker venn vennplot genomicranges granges
7.8 years ago enricoferrero ▴ 660
8
votes
3
replies
1.4k
views
Counting ambiguously mapped reads per feature
rnaseq bam genomicranges GenomicAlignments Rsamtools
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 110
1
vote
3
replies
967
views
Extract information from GenomicRanges
genomicranges genomicfeatures
8.1 years ago ribioinfo ▴ 100
6
votes
2
replies
4.7k
views
How to get the intersect and get the difference of a grange object while keeping meta data
genomicranges intersect
updated 7.9 years ago by 3.8k • written 8.0 years ago by ▴ 30
9
votes
21
replies
11k
views
annotate GRanges with upstream or downstream nearest gene
GRange genomicranges genomicfeatures
updated 8.3 years ago by ★ 1.3k • written 8.3 years ago by ▴ 190
0
votes
5
replies
2.5k
views
brief quesion on DESeq2
Clustering GenomicRanges DESeq2 Clustering GenomicRanges DESeq2
updated 11.0 years ago by ▴ 20 • written 11.1 years ago by 41k
0
votes
5
replies
1.5k
views
how to annotate GenomicRanges objects with genome build
grangeslist rangedsummarizedexperiment parathyroidSE genomicranges granges
8.1 years ago Levi Waldron ★ 1.1k
1
vote
3
replies
1.0k
views
Positions to genes in minfi
genomicranges minfi
7.8 years ago • updated 7.7 years ago Asma rabe ▴ 290
3
votes
5
replies
1.3k
views
How to sort set of GRanges object in the list by increasing order?
granges grangeslist genomicranges
7.8 years ago • updated 7.7 years ago Jurat Shahidin ▴ 80
5
votes
3
replies
1.3k
views
How to avoid repeated overlap pair for GRanges object in grid?
r genomicranges
7.7 years ago • updated 7.5 years ago Jurat Shahidin ▴ 80
19
votes
10
replies
18k
views
How do I merge a list of GRanges?
GenomicRanges
updated 2.2 years ago by ▴ 40 • written 7.8 years ago by ▴ 40
3
votes
4
replies
5.2k
views
GenomicRanges: Take union of GRanges and keep metadata?
GRange genomicranges
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 40
2
votes
5
replies
3.7k
views
GRanges - add names when constructing a new GRanges, rather than afterwards?
genomicranges
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ▴ 740
3
votes
7
replies
2.0k
views
Intersecting a Granges and a GRangesList elementwise
findoverlaps genomicranges
updated 8.7 years ago by 16k • written 8.7 years ago by ▴ 150
4
votes
6
replies
1.7k
views
GenomicRanges mapply to all combinations of GRangesList objects
genomicranges mapply grangeslist
8.5 years ago francesca casalino ▴ 50
5
votes
6
replies
9.3k
views
Merge multiple genomic intervals if overlapping more than xx percents
genomicranges
written 8.9 years ago by ▴ 140
5
votes
8
replies
3.3k
views
Large disk images of DESeqDataSet / SummarizedExperiment objects when using the save function
SummarizedExperiment DESeqDataSet GenomicRanges DESeq2 save
updated 9.2 years ago by ★ 13k • written 9.2 years ago by ▴ 30
2
votes
12
replies
1.9k
views
nearest without overlapping
genomicranges
updated 5.8 years ago by 16k • written 5.8 years ago by ▴ 40
8
votes
12
replies
5.5k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 21 months ago by • 0 • written 9.1 years ago by ▴ 20
0
votes
7
replies
1.2k
views
distanceToNearest for GRanges?
Cancer GenomicRanges Cancer GenomicRanges
updated 12.0 years ago by ▴ 420 • written 12.0 years ago by ★ 6.8k
0
votes
8
replies
1.9k
views
good news and bad news
Infrastructure Cancer IRanges GenomicRanges Infrastructure Cancer IRanges GenomicRanges
updated 11.7 years ago by ★ 13k • written 11.7 years ago by 16k
3
votes
2
replies
1.9k
views
Subset SummarizedExperiment/GRangesList by seqnames
genomicranges
updated 9.0 years ago by ▴ 60 • written 9.0 years ago by 41k
2
votes
7
replies
4.1k
views
coverage over specific GenomicRanges
genomicranges
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 90
0
votes
8
replies
2.4k
views
Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges
GenomicRanges GenomicRanges
updated 11.2 years ago by ★ 13k • written 11.2 years ago by ▴ 740
1
vote
3
replies
2.3k
views
summarizeOverlaps bplapply error
genomicalignments genomicranges bioconductor rnaseq
updated 8.7 years ago by • 0 • written 9.2 years ago by • 0
1
vote
10
replies
2.5k
views
GenomicRanges bug in follow?
genomicranges
8.6 years ago • updated 8.5 years ago Janet Young ▴ 740
0
votes
7
replies
1.7k
views
Probe ID to Sequence
SNPlocs GenomicRanges SNPlocs GenomicRanges
updated 12.7 years ago by ★ 4.2k • written 12.7 years ago by ▴ 400
3
votes
6
replies
2.6k
views
Assign genes to CpG islands
annotation genomicranges bsgenome
updated 8.5 years ago by ★ 1.3k • written 8.5 years ago by ▴ 10
0
votes
6
replies
1.2k
views
wishlist for readGappedAlignments
GenomicRanges Rsamtools GenomicRanges Rsamtools
updated 12.7 years ago by 25k • written 12.7 years ago by ▴ 420
0
votes
2
replies
6.3k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 10.5 years ago by ★ 11k • written 10.5 years ago by 16k
50 results • Page 1 of 1
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Replies
Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference by ATpoint ★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by Gayatri • 0
What I meant is even after deleting the NCBI.sqlite file, and re-running the script, an empty NCBI.sqlite file (0 kb) is created which is c…
Comment: DESeq2 output used for PCA plot on R studio by ATpoint ★ 4.0k
> Increase variability for mutants: use larger subtractive modifiers I was thinking the same as swbarnes. You're doing some data munging h…
Votes
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
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