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 8.5 years ago by ★ 11k • written 8.5 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
8.7 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 8.7 years ago by ★ 6.6k • written 8.7 years ago by ▴ 50
0
votes
3
replies
1.7k
views
Nice plot of gene region (plotTracks function)
gviz granges plottracks
8.7 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 8.9 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 9.1 years ago by 25k • written 9.1 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
886
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 9.5 years ago by ★ 11k • written 9.5 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
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Comment: Using DESeq2 for age prediction by ATpoint ★ 5.0k
You sure will find online tutorials on regression models / machine learning classifiers. The support site is for help with Bioconductor. Ch…
Comment: Using DESeq2 for age prediction by picasa1983 • 0
Thanks ! Do you have any idea how to do that ?
Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
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