Showing : Genomicranges • reset
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
3
votes
21
replies
2.8k
views
`precede` does not perform as expected
genomicranges precede ph525.5x
7.3 years ago wcstcyx ▴ 30
5
votes
14
replies
2.3k
views
Subsetting a GenomicRanges::GRanges with "%in%" fails
genomicranges
4.6 years ago Aditya ▴ 160
1
vote
14
replies
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
3
votes
13
replies
2.3k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder genomicfeatures genomicranges
updated 6.7 years ago by ★ 1.0k • written 6.7 years ago by ▴ 20
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
12
replies
5.4k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 21 months ago by • 0 • written 9.1 years ago by ▴ 20
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
2
votes
12
replies
1.7k
views
remove set number of nucleotides from each gene's cds region in GRangesList
genomicranges genomicfeatures
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ▴ 90
7
votes
12
replies
2.3k
views
Extract isoform-specific ranges
bioconductor genomicranges
updated 6.7 years ago by ★ 1.6k • written 6.7 years ago by ▴ 10
6
votes
12
replies
1.8k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
5.2 years ago foehn ▴ 100
0
votes
12
replies
2.4k
views
more stupid *Ranges questions...
Transcription ChIPpeakAnno GenomicRanges Transcription ChIPpeakAnno GenomicRanges
updated 12.6 years ago by ★ 11k • written 12.6 years ago by ★ 4.2k
9
votes
11
replies
4.2k
views
looping through a GRangesList object
GenomicRanges GRangesList
updated 8.2 years ago by ★ 1.3k • written 8.2 years ago by ★ 3.7k
1
vote
11
replies
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
2
votes
10
replies
1.8k
views
Reorder exons on negative strand in GRanges list
genomicranges
updated 7.9 years ago by ★ 11k • written 7.9 years ago by ▴ 90
5
votes
10
replies
3.0k
views
tileGenome for overlapping ranges?
genomicranges
updated 8.7 years ago by • 0 • written 9.2 years ago by ▴ 740
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
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
10
replies
1.6k
views
Calculate Outer Positions of GappedAlignmentPairs
Coverage GenomicRanges Coverage GenomicRanges
updated 11.1 years ago by ★ 11k • written 11.1 years ago by ★ 1.5k
4
votes
10
replies
3.3k
views
mapCoords for converting genomic coordinates to cDNA coordinates?
genomicranges
updated 9.5 years ago by ★ 6.8k • written 9.5 years ago by ▴ 10
0
votes
10
replies
2.0k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
6.8 years ago lovro0 ▴ 10
2
votes
10
replies
2.2k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 8.4 years ago by ★ 11k • written 8.4 years ago by ▴ 10
3
votes
10
replies
6.7k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
4.8 years ago • updated 4.7 years ago Robert ▴ 10
9
votes
9
replies
3.1k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.3 years ago by 65k • written 2.3 years ago by ▴ 10
4
votes
9
replies
1.6k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 4.6 years ago by 65k • written 4.6 years ago by • 0
0
votes
9
replies
2.1k
views
using a gtf file to map reads
GenomicRanges DESeq2 GenomicRanges DESeq2
updated 10.9 years ago by ★ 11k • written 10.9 years ago by ▴ 300
0
votes
9
replies
1.4k
views
ReportingTools - trouble incorporating annotations
Annotation edgeR GenomicRanges Annotation edgeR GenomicRanges
updated 10.8 years ago by 65k • written 10.8 years ago by ▴ 300
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
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
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
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
2
votes
8
replies
5.3k
views
GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
genomicranges overlap intersect findoverlaps
6.3 years ago Caroline Grisbach Meissner ▴ 10
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
1
vote
8
replies
1.4k
views
Aggregating scores of multiple metadata columns from one GRanges object on another
GenomicRanges
updated 5.1 years ago by ★ 11k • written 5.1 years ago by • 0
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
6
votes
8
replies
2.7k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 5.2 years ago by 25k • written 5.2 years ago by ▴ 80
0
votes
7
replies
2.1k
views
VariantTools installation problem: dependencies not available
IRanges GenomicRanges VariantTools XVector IRanges GenomicRanges VariantTools XVector
updated 10.4 years ago by ★ 11k • written 10.4 years ago by ▴ 360
0
votes
7
replies
1.2k
views
rtracklayer cannot export empty BED file
rtracklayer bed genomicranges
updated 5.4 years ago by ★ 11k • written 5.4 years ago by ▴ 100
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
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
3
votes
7
replies
2.0k
views
Intersecting a Granges and a GRangesList elementwise
findoverlaps genomicranges
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 150
0
votes
7
replies
2.0k
views
regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder GenomeInfoDb GenomicRanges
7.0 years ago Wayne • 0
0
votes
7
replies
3.2k
views
GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
S4Vectors GenomicRanges BiocManager
4.5 years ago james.dalgleish ▴ 30
0
votes
7
replies
1.8k
views
multicore and GRangesList
GenomicRanges GenomicRanges
updated 13.3 years ago by 25k • written 13.3 years ago by ▴ 200
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
7
replies
1.8k
views
Speeding up or replacing Loops to process Bam Reads
genomicranges reads genomicfeatures Bam
9.1 years ago gen ▴ 30
3
votes
7
replies
1.5k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 30
4
votes
6
replies
1.6k
views
GenomicRanges mapply to all combinations of GRangesList objects
genomicranges mapply grangeslist
8.5 years ago francesca casalino ▴ 50
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
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
50 results • Page 1 of 1
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Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Comment: Error retrieving ensembl gene id using biomaRt... by James W. MacDonald 65k
Or that. ;-D
Answer: Error retrieving ensembl gene id using biomaRt... by Mike Smith ★ 6.5k
I think you have the assignment operator (`<-`) the wrong way round. It should be `df_biomrt_tmp <- getBM(...`
Answer: Error retrieving ensembl gene id using biomaRt... by James W. MacDonald 65k
I can't reproduce. ``` > library(biomaRt) Warning message: package 'biomaRt' was built under R version 4.3.2 > library(org.Hs.eg.db…
Comment: DESeq2 setting significant p-value by Michael Love 41k
``` > counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL)) > coldata <- data.frame(x=1:4) > DESeqDataSetFromMatrix(counts, cold…
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Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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