Showing : Granges • reset
28
votes
43
replies
8.4k
views
Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
findoverlaps granges
updated 8.0 years ago by 25k • written 8.2 years ago by ▴ 80
8
votes
7
replies
7.8k
views
Combining two GRangesLists
GRanges grangeslist
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 20
17
votes
4
replies
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
4
votes
8
replies
1.5k
views
the closest gene to a breakpoint
granges plyranges
updated 5.7 years ago by 50k • written 5.7 years ago by ▴ 670
0
votes
3
replies
1.1k
views
View of subsequences corresponding granges on +ve strand and rev. complementary of seq on -ve strand.
Views granges grangeslist iranges
updated 8.5 years ago by 16k • written 8.5 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
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
8
votes
3
replies
3.8k
views
How do I subset a GRanges object based on chromosome (and approximate region)?
GRanges
updated 3.6 years ago by ▴ 120 • written 3.6 years ago by ▴ 10
8
votes
8
replies
8.1k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 4.7 years ago by ▴ 40 • written 8.5 years ago by ▴ 50
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
0
votes
6
replies
6.2k
views
GRanges: problem with multiple seqnames and seqlengths
GRanges seqnames seqlengths IRanges
9.6 years ago topher.hamm • 0
10
votes
8
replies
2.6k
views
Transitive overlaps of GRanges object
granges findOverlaps
updated 9.2 years ago by 16k • written 9.2 years ago by ▴ 40
3
votes
10
replies
6.8k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
4.8 years ago Robert ▴ 10
2
votes
10
replies
3.5k
views
Extract three types of intergenic regions
granges views annotation iranges
updated 8.5 years ago by ★ 1.7k • written 8.5 years ago by ▴ 50
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
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
14
votes
19
replies
19k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 2.2 years ago by ▴ 60 • written 9.5 years ago by ▴ 120
0
votes
4
replies
1.7k
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
6
votes
4
replies
2.0k
views
unlist a exons GRangeslist object and add a gene name column
granges grangeslist txdb.hsapiens.ucsc.hg19.knowngene
updated 6.5 years ago by 16k • written 6.5 years ago by ▴ 190
0
votes
7
replies
2.2k
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 5.7 years ago by • 0 • written 5.7 years ago by • 0
1
vote
2
replies
3.5k
views
about appending GRANGES
GRanges
9.4 years ago Bogdan ▴ 670
2
votes
3
replies
1.4k
views
How to find nearest CpG islands around miRNA genes using granges?
granges bioconductor R
6.7 years ago Adam_M • 0
0
votes
2
replies
1.4k
views
"for loop" and AUTOPLOT function
ggbio granges
9.4 years ago Bogdan ▴ 670
0
votes
3
replies
3.6k
views
makeTxDbFromGFF Error: subscript contains NAs
genomicfeatures granges maketxdbfromgff
updated 6.6 years ago by 16k • written 6.8 years ago by • 0
2
votes
3
replies
7.6k
views
GRanges - changing seqlevels
granges seqlevels
9.0 years ago Hermann Norpois ▴ 170
3
votes
2
replies
1.3k
views
gene model generation support?
granges gene models GenomicFeatures
9.0 years ago • updated 8.7 years ago Vincent J. Carey, Jr. 6.7k
0
votes
3
replies
1.5k
views
Using IRanges to find gene TSS that overlap a window
iranges R granges
updated 6.7 years ago by • 0 • written 6.7 years ago by ▴ 20
6
votes
2
replies
772
views
Combine 5' leaders and 1st exon of cds into GRangesList
GRanges mapToTranscripts
6.5 years ago hauken_heyken ▴ 80
0
votes
6
replies
3.8k
views
GRanges::distanceToNearest does not return distance to nearest
granges genomicranges
updated 6.3 years ago by ★ 6.8k • written 6.4 years ago by ▴ 40
2
votes
5
replies
1.2k
views
DistanceToNearest Not giving nearest Range
GRanges distancetonearest
updated 6.4 years ago by ★ 4.3k • written 6.4 years ago by ▴ 10
4
votes
17
replies
3.2k
views
How to construct a valid GRanges object from RCPP and pass back to R
GRanges IRanges RCPP Constructor
updated 6.5 years ago by ▴ 10 • written 6.6 years ago by ▴ 80
22
votes
10
replies
7.4k
views
Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges chippeakanno
updated 7.1 years ago by ▴ 10 • written 7.1 years ago by ▴ 80
3
votes
5
replies
17k
views
Any quick solution for fixing error : "$ operator is invalid for atomic vectors" ?
r granges dplyr error handling
updated 7.5 years ago by ★ 6.5k • written 7.5 years ago by ▴ 80
3
votes
5
replies
1.3k
views
How to sort set of GRanges object in the list by increasing order?
granges grangeslist genomicranges
7.7 years ago Jurat Shahidin ▴ 80
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 9 days ago by • 0 • written 8.0 years ago by ▴ 170
5
votes
2
replies
1.3k
views
Using GRanges and IRanges to simply get all chromosome data
GRanges IRanges
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 30
2
votes
2
replies
1.1k
views
Findoverlaps insame sample
genomicranges granges findoverlaps
7.0 years ago julrodr80 ▴ 30
0
votes
2
replies
2.8k
views
rtracklayer /GRange object to BED format?
granges rtracklayer
updated 8.2 years ago by ★ 11k • written 8.2 years ago by ▴ 80
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
2
votes
5
replies
2.1k
views
Intersecting a Granges and a GRangesList using within
granges grangeslist findoverlaps
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 150
3
votes
5
replies
4.2k
views
GRanges returning warning message: 'ranges' contains values outside of sequence bounds.
granges
updated 9.4 years ago by 16k • written 9.5 years ago by ▴ 10
3
votes
4
replies
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
5
replies
2.6k
views
import wig to coverage
rtracklayer granges import.wig
updated 9.2 years ago by 16k • written 9.2 years ago by ▴ 140
2
votes
3
replies
2.3k
views
ggbio circular plot
ggbio SNP granges
updated 8.3 years ago by ★ 11k • written 8.4 years ago by • 0
6
votes
6
replies
2.5k
views
Memory-efficient method to calculate GC content of millions of GRanges
granges biostrings bsapply BSgenome
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 70
4
votes
3
replies
2.1k
views
Overlap the snps
overlap snps granges iranges
updated 9.6 years ago by ★ 11k • written 9.6 years ago by ▴ 10
6
votes
11
replies
7.3k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges split r
updated 2.4 years ago by ▴ 40 • written 8.2 years ago by ▴ 80
5
votes
9
replies
1.8k
views
reduce function after combining 2 GRanges objects from cn.mops output
GRanges cn.mops
updated 6.8 years ago by ★ 11k • written 6.8 years ago by ▴ 110
1
vote
5
replies
1.5k
views
Coerce several Granges objects to a GrangeList
GRanges GRangesList ChIP
9.6 years ago patrick.schordert ▴ 30
9
votes
38
replies
6.7k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.2 years ago by ▴ 190
50 results • Page 1 of 1
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Answer: List of Deprecated Packages for Bioc3.19 by shepherl 3.8k
singleCellTK has been fixed and will remain in Bioconductor
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
Yes, I'm working only with genes from terpenoids pathway (14 genes), so I can't use enrichGO? Can you recommend a package or something like…
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
Your awnser at Cannabis orgDb solve my problems using enrichGO by far. I'm underdegree biotechnology student, and I learning bioinformatic…
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
It is indeed better. Anyway, did you notice this part in the output from `str(ortologos_filtrados)`: `$Gene.ID : int 115709372 115716460 …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
I'm new here, but its better now?
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Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
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Comment: DESeq2 - dispersion estimation when there is none
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