Showing : Granges • reset
4
votes
3
replies
5.9k
views
What is the proper way to modify mcols of a GRanges inside a GRangesList?
granges metadata
updated 8.4 years ago by ★ 11k • written 8.4 years ago by ★ 7.9k
1
vote
1
reply
1.2k
views
Obtain exactly the interval that overlap
findoverlaps Granges
updated 8.5 years ago by ★ 11k • written 8.5 years ago by ▴ 30
2
votes
3
replies
1.7k
views
Split Genomic Ranges With Reference Overlaps (Centromere)
granges genomicranges split
written 8.5 years ago by • 0
2
votes
2
replies
1.4k
views
Findoverlaps insame sample
genomicranges granges findoverlaps
8.5 years ago julrodr80 ▴ 30
4
votes
2
replies
1.7k
views
trying to annotate overlaps with external file information
iranges granges
updated 8.5 years ago by ★ 11k • written 8.5 years ago by ▴ 50
0
votes
2
replies
1.7k
views
Error in GRanges strand input
GRanges Tutorial
updated 8.5 years ago by 25k • written 8.5 years ago by • 0
0
votes
4
replies
1.6k
views
Data structure for my dataset
metadata grangeslist granges sample
updated 8.5 years ago by ★ 11k • written 8.5 years ago by • 0
2
votes
4
replies
5.6k
views
What is the best way to subset a DNAStringSet by a GRange ?
bioconductor biostrings granges
updated 8.6 years ago by ★ 11k • written 8.6 years ago by • 0
22
votes
10
replies
8.3k
views
Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges chippeakanno
updated 8.6 years ago by ▴ 10 • written 8.6 years ago by ▴ 80
0
votes
32
replies
5.6k
views
Identify repetitive sequences in 10kbp promoter region in Mouse
granges short tandem repetitions repeat
8.8 years ago • updated 8.7 years ago mkmb2004 • 0
1
vote
4
replies
1.5k
views
pROBLEMS WITH findOverlapPairs
gRANGES iranges findoverlaps
updated 8.7 years ago by 68k • written 8.7 years ago by ▴ 30
4
votes
3
replies
6.4k
views
Splitting a GRanges object into List of GRange objects by position.
R granges subsett grangeslist group
updated 8.8 years ago by ★ 6.6k • written 8.8 years ago by ▴ 50
0
votes
3
replies
1.7k
views
Nice plot of gene region (plotTracks function)
gviz granges plottracks
8.8 years ago Adam • 0
6
votes
4
replies
1.7k
views
Aggregate read counts by non-uniform overlapping sliding windows
granges genomicranges featurecounts
updated 8.8 years ago by ★ 11k • written 8.8 years ago by ▴ 20
6
votes
6
replies
3.0k
views
Memory-efficient method to calculate GC content of millions of GRanges
granges biostrings bsapply BSgenome
updated 9.0 years ago by 16k • written 9.0 years ago by ▴ 70
8
votes
7
replies
9.7k
views
Combining two GRangesLists
GRanges grangeslist
updated 9.0 years ago by 25k • written 9.0 years ago by ▴ 20
0
votes
5
replies
1.8k
views
GRanges nearest fails for non-overlapping regions
bug genomicranges granges nearest
9.0 years ago dondelelcaro ▴ 10
2
votes
2
replies
1.3k
views
Any way to speed up splitting relatively big GRanges objects by given threshold ?
r granges split performance
updated 9.0 years ago by ★ 11k • written 9.0 years ago by ▴ 80
3
votes
5
replies
19k
views
Any quick solution for fixing error : "$ operator is invalid for atomic vectors" ?
r granges dplyr error handling
updated 9.0 years ago by ★ 6.6k • written 9.0 years ago by ▴ 80
1
vote
1
reply
1.5k
views
Add main title to ggbio's karyogram
ggbio karyogram granges
updated 9.1 years ago by ★ 11k • written 9.1 years ago by ▴ 80
0
votes
3
replies
2.2k
views
Efficiently construct GRanges/IRanges from Rle vector
Rle granges iranges
9.1 years ago my4 ▴ 10
2
votes
1
reply
1.3k
views
Function to convert genomic ranges to browser-friendly coordinates ?
granges coordinate genome browser
updated 9.1 years ago by ★ 11k • written 9.1 years ago by ▴ 180
3
votes
3
replies
1.6k
views
aggregate bins in large SummarizedExperiment efficiently
granges summarizedexperiment reduce
updated 9.1 years ago by ★ 11k • written 9.1 years ago by ▴ 20
5
votes
2
replies
1.9k
views
Using GRanges and IRanges to simply get all chromosome data
GRanges IRanges
updated 9.2 years ago by 25k • written 9.2 years ago by ▴ 30
0
votes
4
replies
1.5k
views
apply over the 'rows' of a GRanges object (and/or: is there a fiveprime() function for GRanges objects?)
granges genomicranges
updated 9.2 years ago by ★ 11k • written 9.2 years ago by ▴ 160
1
vote
2
replies
1.4k
views
Locating enhancers that are mutated
snv granges genomicranges variantannotation indel
updated 9.2 years ago by ★ 11k • written 9.2 years ago by • 0
1
vote
2
replies
2.5k
views
Subsetting GRanges based on metadata
GRanges metadata subsetting
updated 9.2 years ago by ★ 11k • written 9.2 years ago by ▴ 10
0
votes
1
reply
889
views
How to use GRanges to find locations that do NOT overlap?
granges
updated 9.2 years ago by ★ 11k • written 9.2 years ago by • 0
3
votes
3
replies
1.5k
views
Find hits of subject that start somewhere in the query by using GRanges / IRanges and findOverlap()
IRanges GRanges findoverlaps R
updated 9.2 years ago by ★ 11k • written 9.2 years ago by • 0
3
votes
2
replies
1.9k
views
Keep original range by using flank() on a GRanges object.
granges flank
updated 9.2 years ago by ★ 6.8k • written 9.2 years ago by • 0
2
votes
2
replies
1.8k
views
GRanges get hits from (only) antisense strand with findOverlaps().
GRanges findoverlaps antisense
updated 9.2 years ago by ▴ 450 • written 9.2 years ago by • 0
3
votes
5
replies
1.9k
views
How to sort set of GRanges object in the list by increasing order?
granges grangeslist genomicranges
9.3 years ago Jurat Shahidin ▴ 80
0
votes
1
reply
2.0k
views
Efficient coverage calculation with RleList and GRanges
granges Rle coverage View mean
updated 9.3 years ago by ★ 11k • written 9.3 years ago by ▴ 170
3
votes
4
replies
2.7k
views
ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds
chipseeker venn vennplot genomicranges granges
9.3 years ago enricoferrero ▴ 680
4
votes
10
replies
10k
views
How can I extract sequences from a FASTA file for each of the intervals defined in a BED file using R?
R bioconductor granges
9.7 years ago • updated 9.3 years ago pertille • 0
4
votes
1
reply
4.0k
views
Collapse/Reduce in GRanges by Metadata Column
granges merge reduce
updated 9.3 years ago by ★ 11k • written 9.3 years ago by • 0
3
votes
9
replies
2.5k
views
find next non-overlapping nth elements of a given region
biomart granges findoverlaps
updated 9.4 years ago by ★ 11k • written 9.4 years ago by ▴ 20
15
votes
4
replies
13k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 3.6 years ago by 16k • written 9.4 years ago by ▴ 40
3
votes
7
replies
2.5k
views
Group GRanges and keep metadata
granges metadata coursera
updated 9.4 years ago by ★ 11k • written 9.4 years ago by ▴ 10
6
votes
10
replies
3.2k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 18 months ago by • 0 • written 9.5 years ago by ▴ 180
4
votes
2
replies
1.5k
views
Get internal exons using GenomicFeatures
genomicfeatures granges
updated 9.5 years ago by ★ 11k • written 9.5 years ago by ▴ 10
5
votes
8
replies
3.1k
views
closest-features equivalent in Bioconductor for finding closest gene(s)
genomicranges granges iranges annotatepeak
updated 9.5 years ago by ★ 11k • written 9.5 years ago by ▴ 80
4
votes
1
reply
1.6k
views
convert XStringViews into GRanges
GRanges XStringViews
updated 9.5 years ago by ★ 11k • written 9.5 years ago by ▴ 40
28
votes
43
replies
10k
views
Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
findoverlaps granges
updated 9.5 years ago by 25k • written 9.7 years ago by ▴ 80
1
vote
4
replies
1.6k
views
calculate total transcript length from DisjointExons output (Genomic Ranges Object)
genomicfeatures non overlapping exons genomicranges granges
updated 9.6 years ago by ★ 11k • written 9.6 years ago by ▴ 30
9
votes
6
replies
3.6k
views
Any method can coerce "list" object to GRanges [reproducible example is included]?
granges error handling R
updated 9.6 years ago by ★ 11k • written 9.6 years ago by ▴ 80
0
votes
2
replies
2.6k
views
Help with toGRanges
granges chippeakanno
updated 9.6 years ago by ★ 1.6k • written 9.6 years ago by • 0
1
vote
2
replies
2.0k
views
Combining GRange/VRange objects
granges vranges readvcfasvranges somaticsignatures
updated 9.6 years ago by ★ 11k • written 9.6 years ago by • 0
3
votes
6
replies
1.5k
views
How to replace NAs values in "CompressedIntegerList" objects [reproducible example is included] ?
r bug granges
9.6 years ago Jurat Shahidin ▴ 80
0
votes
4
replies
3.8k
views
[Solved]Preserve metadata column for retrieving common regions from two GRanges objects
granges intersect
9.6 years ago Jurat Shahidin ▴ 80
206 results • Page 3 of 5
Recent ...
Replies
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Votes
Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Awards • All
Popular Question to shepherl 4.2k
Popular Question to Hervé Pagès 16k
Popular Question to Ou, Jianhong ★ 1.3k
Popular Question to Maria Doyle ▴ 100
Popular Question to Gordon Smyth 53k
Locations • All
USA, Los Angeles, USC, 11 minutes ago
The city by the bay, 26 minutes ago
WEHI, Melbourne, Australia, 36 minutes ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 1017 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6