Showing : genomicranges • reset
4
votes
4
replies
5.3k
views
How to bin a GRanges to small bins
GenomicRanges
updated 9.9 years ago by ★ 11k • written 9.9 years ago by ▴ 200
9
votes
21
replies
13k
views
annotate GRanges with upstream or downstream nearest gene
GRange genomicranges genomicfeatures
updated 9.9 years ago by ★ 1.3k • written 9.9 years ago by ▴ 200
1
vote
4
replies
1.8k
views
subsetting a GRanges object with IntegerList and CharacterList metadata columns
granges genomicranges
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 10
1
vote
2
replies
1.3k
views
How to find similar ranges without algorithm="intervaltree"
granges genomicranges iranges
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 40
2
votes
2
replies
1.5k
views
Efficiently finding a relative position inside a GRanges object
genomicranges
10.0 years ago Aliaksei Holik ▴ 350
2
votes
10
replies
3.0k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 10
0
votes
1
reply
1.8k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 4.0 years ago by • 0 • written 10.0 years ago by ▴ 10
4
votes
5
replies
4.1k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 22 months ago by ▴ 10 • written 10.0 years ago by ▴ 10
1
vote
11
replies
3.0k
views
Had to remove duplicated() in order to install GenomicRanges 1.22 on top of 1.20 on linux
installation genomicranges summarizedexperiment
10.1 years ago • updated 10.0 years ago knb • 0
1
vote
3
replies
2.3k
views
issue renaming seqnames in genomic ranges
genomicranges
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 90
1
vote
1
reply
1.0k
views
Concatenate individual genomic intervals into populational regions
genomicranges
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 40
1
vote
6
replies
2.8k
views
Error: subsetting GenomicRanges with disjoint ranges produces errors
software error genomicranges
10.0 years ago ripkrizbi • 0
3
votes
2
replies
2.2k
views
how much positions overlapped for each pair of the pairs obtained by findoverlap.
granges genomicranges findoverlaps subsetbyoverlaps
updated 10.1 years ago by 16k • written 10.1 years ago by ▴ 50
1
vote
10
replies
3.3k
views
GenomicRanges bug in follow?
genomicranges
10.2 years ago • updated 10.1 years ago Janet Young ▴ 740
0
votes
6
replies
5.5k
views
Package ‘GenomicRanges’ version 1.20.8 cannot be unloaded
rapidr genomicranges
10.1 years ago Pau Marc Muñoz Torres ▴ 20
3
votes
6
replies
3.2k
views
Assign genes to CpG islands
annotation genomicranges bsgenome
updated 10.1 years ago by ★ 1.3k • written 10.1 years ago by ▴ 10
4
votes
6
replies
2.2k
views
GenomicRanges mapply to all combinations of GRangesList objects
genomicranges mapply grangeslist
10.1 years ago francesca casalino ▴ 50
0
votes
2
replies
990
views
Package GenomicRanges missing functions and classes related to Gapped Alignments
genomicranges
10.1 years ago jduffner • 0
4
votes
2
replies
1.9k
views
How to find particular types of overlap with GenomicRanges
r genomicranges iranges
updated 10.1 years ago by ★ 11k • written 10.1 years ago by ▴ 50
17
votes
4
replies
13k
views
How to use GenomicRanges to find overlaps by percentage covered of interval
genomicranges
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 50
2
votes
5
replies
4.9k
views
GRanges - add names when constructing a new GRanges, rather than afterwards?
genomicranges
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 740
2
votes
2
replies
1.5k
views
Can precede() and follow() in some cases return identical output?
genomicranges
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Feature Request: improve output when printing GenomicRanges instances
GenomicRanges featurerequest
10.2 years ago Keith Hughitt ▴ 180
3
votes
7
replies
2.7k
views
Intersecting a Granges and a GRangesList elementwise
findoverlaps genomicranges
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 150
1
vote
1
reply
2.1k
views
Using findOverlaps to find only partial overlaps
findoverlaps genomicranges
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 150
2
votes
12
replies
2.5k
views
remove set number of nucleotides from each gene's cds region in GRangesList
genomicranges genomicfeatures
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 90
0
votes
2
replies
2.4k
views
Problem with Finding Mean Coverage using binnedAverage function
GenomicRanges
updated 10.2 years ago by 16k • written 10.2 years ago by • 0
5
votes
10
replies
4.1k
views
tileGenome for overlapping ranges?
genomicranges
updated 10.3 years ago by • 0 • written 10.8 years ago by ▴ 740
0
votes
3
replies
1.8k
views
narrow function for GRangesList objects?
genomicranges
10.3 years ago Janet Young ▴ 740
1
vote
3
replies
2.7k
views
summarizeOverlaps bplapply error
genomicalignments genomicranges bioconductor rnaseq
updated 10.3 years ago by • 0 • written 10.8 years ago by • 0
8
votes
9
replies
6.8k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 10.4 years ago by • 0 • written 10.4 years ago by ★ 1.5k
0
votes
6
replies
4.0k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster quasR genomicfeatures genomicranges alignment
updated 10.4 years ago by 16k • written 10.4 years ago by ▴ 70
1
vote
2
replies
2.4k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 10.4 years ago by 25k • written 10.4 years ago by ▴ 90
11
votes
0
replies
6.5k
views
Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
10.4 years ago Martin Morgan 25k
2
votes
7
replies
5.1k
views
coverage over specific GenomicRanges
genomicranges
updated 10.4 years ago by 16k • written 10.4 years ago by ▴ 90
1
vote
1
reply
3.8k
views
bedtools like subtract in genomic ranges?
genomicranges
updated 10.4 years ago by 25k • written 10.4 years ago by ▴ 90
0
votes
1
reply
1.9k
views
Newbie - Adding Labels to Individual Genes with ggbio?
r ggbio ggplot2 dnaseq genomicranges
updated 10.4 years ago by ▴ 130 • written 10.4 years ago by • 0
1
vote
2
replies
1.1k
views
GRanges / IRanges maxgap behaviour change raises no warning
genomicranges granges iranges
updated 10.5 years ago by 16k • written 10.5 years ago by ▴ 40
5
votes
6
replies
11k
views
Merge multiple genomic intervals if overlapping more than xx percents
genomicranges
written 10.5 years ago by ▴ 140
3
votes
2
replies
2.2k
views
Subset SummarizedExperiment/GRangesList by seqnames
genomicranges
updated 10.6 years ago by ▴ 70 • written 10.6 years ago by 43k
17
votes
4
replies
18k
views
How to properly sort GRanges?
granges genomicranges sort seqnames order
updated 10.6 years ago by ▴ 30 • written 11.0 years ago by ▴ 680
0
votes
2
replies
2.2k
views
Calculate the expression of gene
genomicranges iranges
updated 10.7 years ago by 68k • written 10.7 years ago by ▴ 20
0
votes
7
replies
2.4k
views
Speeding up or replacing Loops to process Bam Reads
genomicranges reads genomicfeatures Bam
10.7 years ago gen ▴ 30
0
votes
3
replies
2.8k
views
problem with cbind on GRanges object - new bug?
genomicranges cbind
10.7 years ago Janet Young ▴ 740
2
votes
1
reply
2.6k
views
Change the start of GenomicRanges list
genomicranges
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 90
1
vote
1
reply
1.5k
views
removing reads from coverage() calculation.
bam rsamtools genomicranges
updated 10.8 years ago by 25k • written 10.8 years ago by ▴ 30
5
votes
8
replies
3.9k
views
Large disk images of DESeqDataSet / SummarizedExperiment objects when using the save function
SummarizedExperiment DESeqDataSet GenomicRanges DESeq2 save
updated 10.8 years ago by ★ 13k • written 10.8 years ago by ▴ 30
4
votes
1
reply
7.8k
views
how to get genomic coordinates for a list of genes
genomicranges
updated 10.8 years ago by 21k • written 10.8 years ago by ▴ 50
4
votes
2
replies
3.7k
views
extracting distance from Hits object
genomicranges iranges
updated 10.8 years ago by 16k • written 10.8 years ago by ▴ 140
3
votes
5
replies
3.9k
views
Element-wise setdiff when psetdiff fails for GenomicRanges
genomicranges iranges genomics
updated 10.8 years ago by ▴ 60 • written 10.8 years ago by ▴ 150
403 results • Page 6 of 9
Recent ...
Replies
Answer: mzR-Rcpp compiler version issue by Laurent Gatto 1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co by jamie.gearing ▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria by Stefano Mangiola ▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Answer: DESeq2 design for haplotype MPRA by aimesd808 • 0
I appreciate you telling me about this. Now it's crystal plain to me. Publish this: https://support.bioconductor.org/p/9162649/
Answer: Extract snp information from genomic regions with biomaRt -> "oaries_snp" by Kevin Blighe ★ 4.0k
My sincere apologies that my colleagues had ignored your question. The error occurs because the "chromosomal_region" filter is not valid…
Votes
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Comment: Error installing Seqinfo
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to James W. MacDonald 68k
Locations • All
United States, 4 minutes ago
United States, 53 minutes ago
United States, 57 minutes ago
The city by the bay, 1 hour ago
United States, 1 hour ago
Traffic: 565 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