Showing : granges • reset
0
votes
5
replies
2.1k
views
how to annotate GenomicRanges objects with genome build
grangeslist rangedsummarizedexperiment parathyroidSE genomicranges granges
9.6 years ago Levi Waldron ★ 1.1k
2
votes
2
replies
2.6k
views
How to get list of E.coli genes wit their details on Genome?
biomart maketxdbfrombiomart granges
updated 9.6 years ago by 6.7k • written 9.6 years ago by ▴ 50
0
votes
1
reply
1.6k
views
How to find index position of desired feature_by in TxDb granges?
granges txdb genomicfeatures
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 50
2
votes
2
replies
1.7k
views
How to rename seqlevels style (I, II, III, ...,XVI, Mito to 1,2,3,...16, 17.) in txdb granges?
renameSeqlevels mapSeqlevels grangeslist granges txdb
9.7 years ago vinod.acear ▴ 50
0
votes
1
reply
1.6k
views
Gviz Group of different sizes
gviz R granges
updated 9.7 years ago by ★ 1.6k • written 9.7 years ago by • 0
0
votes
2
replies
3.4k
views
rtracklayer /GRange object to BED format?
granges rtracklayer
updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 80
6
votes
7
replies
5.1k
views
unexpected error when creating GRanges object by calling makeGRangesFromDataFrame()
r error handling granges
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 80
0
votes
2
replies
1.5k
views
GenomicInteractions read in bedpe error
genomicinteractions GRanges
updated 9.7 years ago by ▴ 140 • written 9.7 years ago by ▴ 200
0
votes
1
reply
4.2k
views
Subset VCF files using multiple criteria
vcf variantannotation granges
9.7 years ago georgewwp • 0
6
votes
11
replies
8.7k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges split r
updated 3.9 years ago by ▴ 40 • written 9.8 years ago by ▴ 80
2
votes
3
replies
2.8k
views
ggbio circular plot
ggbio SNP granges
updated 9.9 years ago by ★ 11k • written 9.9 years ago by • 0
1
vote
4
replies
1.8k
views
subsetting a GRanges object with IntegerList and CharacterList metadata columns
granges genomicranges
updated 9.9 years ago by ★ 11k • written 9.9 years ago by ▴ 10
1
vote
2
replies
1.3k
views
How to find similar ranges without algorithm="intervaltree"
granges genomicranges iranges
updated 9.9 years ago by 16k • written 9.9 years ago by ▴ 40
0
votes
1
reply
1.3k
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 9.9 years ago by ★ 29k • written 9.9 years ago by • 0
2
votes
2
replies
3.6k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter granges refseq ucsc organismdb
updated 9.9 years ago by ★ 3.4k • written 9.9 years ago by ▴ 10
6
votes
1
reply
2.4k
views
Retrieving Regions from hg38 of the same GC content and length with a list of elements
regioneR GRanges GCcontent
updated 9.9 years ago by ▴ 150 • written 9.9 years ago by ▴ 80
0
votes
3
replies
1.5k
views
Sampling protein coding genes of the same length distribution as another set of elements using GRanges
granges R sample
updated 10.0 years ago by ★ 1.3k • written 10.0 years ago by ▴ 80
0
votes
3
replies
2.2k
views
I want have a score vector of length of grange that is overlapping with other grange.
granges findoverlaps subsetbyoverlaps
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 50
9
votes
3
replies
5.5k
views
how to extract Granges not overlapping with other ganges?
Granges findoverlaps
updated 10.0 years ago by 68k • written 10.0 years ago by ▴ 50
3
votes
2
replies
2.1k
views
how much positions overlapped for each pair of the pairs obtained by findoverlap.
granges genomicranges findoverlaps subsetbyoverlaps
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 50
2
votes
10
replies
4.5k
views
Extract three types of intergenic regions
granges views annotation iranges
updated 10.0 years ago by ★ 1.7k • written 10.0 years ago by ▴ 50
1
vote
2
replies
1.0k
views
Non overlaps seqence
granges
updated 10.0 years ago by ★ 11k • written 10.0 years ago by • 0
3
votes
3
replies
2.0k
views
Sorting data frame derived from GRanges
granges data.frame sort
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 50
1
vote
13
replies
3.3k
views
Rsamtools memory leak
rsamtools scanbam bam granges iranges
10.0 years ago mhills ▴ 10
0
votes
3
replies
1.6k
views
View of subsequences corresponding granges on +ve strand and rev. complementary of seq on -ve strand.
Views granges grangeslist iranges
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 50
2
votes
5
replies
2.8k
views
Intersecting a Granges and a GRangesList using within
granges grangeslist findoverlaps
updated 10.1 years ago by 16k • written 10.1 years ago by ▴ 150
1
vote
3
replies
1.3k
views
ignore.strand option in range() when using GRangesList
granges
10.1 years ago d r ▴ 150
3
votes
2
replies
1.6k
views
gene model generation support?
granges gene models GenomicFeatures
10.5 years ago • updated 10.2 years ago Vincent J. Carey, Jr. 6.7k
0
votes
1
reply
1.5k
views
circular display in ggbio
ggbio granges
10.3 years ago • updated 10.2 years ago Bogdan ▴ 670
0
votes
4
replies
2.0k
views
browserSession for Arabidopsis
rtracklayer Granges spliceR
updated 10.3 years ago by ★ 11k • written 10.3 years ago by • 0
4
votes
2
replies
1.8k
views
Slice of aligned sequences
bam granges genomicalignments
updated 10.3 years ago by 16k • written 10.3 years ago by ▴ 10
1
vote
2
replies
1.1k
views
GRanges / IRanges maxgap behaviour change raises no warning
genomicranges granges iranges
updated 10.4 years ago by 16k • written 10.4 years ago by ▴ 40
2
votes
5
replies
2.6k
views
From a GRanges object to a GRangeList
granges grangeslist
updated 10.5 years ago by 68k • written 10.5 years ago by ▴ 20
2
votes
3
replies
8.4k
views
GRanges - changing seqlevels
granges seqlevels
10.5 years ago Hermann Norpois ▴ 170
5
votes
3
replies
2.2k
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 10.5 years ago by 16k • written 10.6 years ago by ▴ 10
17
votes
4
replies
18k
views
How to properly sort GRanges?
granges genomicranges sort seqnames order
updated 10.5 years ago by ▴ 30 • written 11.0 years ago by ▴ 680
2
votes
6
replies
3.4k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 10.6 years ago by 25k • written 10.6 years ago by ▴ 30
0
votes
1
reply
1.5k
views
Mean Coverage version of stat_coverage and coverage?
grangeslist granges Genomicfeatures bam
10.6 years ago gen ▴ 30
2
votes
4
replies
2.5k
views
Editing of GAlignments
granges rsamtools bioconductor
updated 10.7 years ago by 25k • written 10.7 years ago by ▴ 30
3
votes
5
replies
3.9k
views
Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
variantannotation granges DNAStringSetList findoverlaps Vranges
10.7 years ago summerela • 0
10
votes
8
replies
3.3k
views
Transitive overlaps of GRanges object
granges findOverlaps
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 40
1
vote
1
reply
1.7k
views
Conversion of BSgenome format to GRanges format?
bsgenome granges bam
updated 10.7 years ago by 68k • written 10.7 years ago by • 0
8
votes
5
replies
3.2k
views
import wig to coverage
rtracklayer granges import.wig
updated 10.7 years ago by 16k • written 10.8 years ago by ▴ 140
4
votes
3
replies
1.3k
views
stacking (partially or completely overlapping) GRanges/IRanges
granges iranges rnaseq
updated 10.7 years ago by 25k • written 10.7 years ago by ★ 2.1k
0
votes
1
reply
1.7k
views
ggbio, overview circular plot, BSgenome, bam to GRanges?
ggbio GRanges ggbio GRanges
10.8 years ago pterry • 0
2
votes
2
replies
1.3k
views
DiffBind individual sample concentrations for differentially bound sites
diffbind granges
updated 10.9 years ago by ★ 5.2k • written 10.9 years ago by ▴ 50
3
votes
5
replies
5.3k
views
GRanges returning warning message: 'ranges' contains values outside of sequence bounds.
granges
updated 10.9 years ago by 16k • written 11.0 years ago by ▴ 10
4
votes
2
replies
2.2k
views
Combine two GRanges to a single GRangesList
granges grangeslist GenomicRanges
updated 10.9 years ago by 25k • written 10.9 years ago by 21k
1
vote
2
replies
4.1k
views
about appending GRANGES
GRanges
10.9 years ago Bogdan ▴ 670
0
votes
2
replies
1.9k
views
"for loop" and AUTOPLOT function
ggbio granges
10.9 years ago Bogdan ▴ 670
206 results • Page 4 of 5
Recent ...
Replies
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Comment: bake() and cool() resulting in an empty table by Francesc • 0
Hi Catherine, thanks so much for using dar and for reporting this bug! We have identified the issue and pushed a fix to the dar repo (PR #…
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
Awards • All
Popular Question to Maria Doyle ▴ 100
Popular Question to Gordon Smyth 53k
Oracle to shepherl 4.2k
Popular Question to Matej • 0
Popular Question to Hervé Pagès 16k
Locations • All
United Kingdom, 1 minute ago
Chile, 7 minutes ago
United States, 20 minutes ago
United States, 1 hour ago
Kenya, 1 hour ago
Traffic: 1131 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