Showing : GenomicRanges • reset
20
votes
10
replies
22k
views
How do I merge a list of GRanges?
GenomicRanges
updated 4.0 years ago by ▴ 40 • written 9.6 years ago by ▴ 40
17
votes
4
replies
19k
views
How to properly sort GRanges?
granges genomicranges sort seqnames order
updated 10.8 years ago by ▴ 30 • written 11.2 years ago by ▴ 680
9
votes
21
replies
14k
views
annotate GRanges with upstream or downstream nearest gene
GRange genomicranges genomicfeatures
updated 10.1 years ago by ★ 1.3k • written 10.1 years ago by ▴ 200
17
votes
4
replies
13k
views
How to use GenomicRanges to find overlaps by percentage covered of interval
genomicranges
updated 10.4 years ago by ★ 11k • written 10.4 years ago by ▴ 50
15
votes
4
replies
13k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 3.9 years ago by 16k • written 9.7 years ago by ▴ 40
10
votes
3
replies
11k
views
resize (shrink/expand) GenomicRanges
GenomicRanges IRanges
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 40
5
votes
8
replies
11k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 4.0 years ago by • 0 • written 10.4 years ago by ▴ 50
5
votes
6
replies
11k
views
Merge multiple genomic intervals if overlapping more than xx percents
genomicranges
written 10.7 years ago by ▴ 140
0
votes
4
replies
10k
views
rtracklayer importing gtf files
rtracklayer DESeq GenomicRanges rtracklayer DESeq GenomicRanges
updated 12.9 years ago by ★ 11k • written 12.9 years ago by ★ 13k
3
votes
10
replies
9.3k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
6.6 years ago Robert ▴ 10
1
vote
3
replies
8.5k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 4.3 years ago by 68k • written 4.3 years ago by ▴ 10
4
votes
1
reply
7.9k
views
how to get genomic coordinates for a list of genes
genomicranges
updated 11.0 years ago by 21k • written 11.0 years ago by ▴ 50
6
votes
6
replies
7.6k
views
converting a GRangesList object with different lengths into a data frame
genomicranges grangeslist dataframe irangeslist lists
updated 8.4 years ago by ★ 11k • written 8.4 years ago by ★ 1.5k
0
votes
2
replies
7.4k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 12.3 years ago by ★ 11k • written 12.3 years ago by 16k
3
votes
4
replies
7.4k
views
Subset GRanges object into new object
R genomicranges subsetting
8.3 years ago jhanks1981 • 0
8
votes
12
replies
7.2k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 3.6 years ago by • 0 • written 10.9 years ago by ▴ 20
11
votes
13
replies
7.1k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
5.2 years ago • updated 5.0 years ago rohitsatyam102 ▴ 20
8
votes
9
replies
7.0k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 10.6 years ago by • 0 • written 10.6 years ago by ★ 1.5k
2
votes
8
replies
6.7k
views
GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
genomicranges overlap intersect findoverlaps
8.1 years ago Caroline Grisbach Meissner ▴ 10
5
votes
2
replies
6.7k
views
setdiff for GenomicRanges
genomicranges
updated 9.4 years ago by ★ 11k • written 9.4 years ago by ★ 4.3k
11
votes
0
replies
6.6k
views
Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
10.6 years ago Martin Morgan 25k
0
votes
2
replies
6.4k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.9 years ago by ▴ 20 • written 3.9 years ago by • 0
3
votes
4
replies
6.4k
views
GenomicRanges: Take union of GRanges and keep metadata?
GRange genomicranges
updated 9.4 years ago by 25k • written 9.4 years ago by ▴ 40
1
vote
1
reply
6.1k
views
Error trying to install GenomicRanges
cummerbund rtracklayer genomicranges s4vectors iranges
updated 10.1 years ago by ★ 6.6k • written 10.1 years ago by • 0
6
votes
2
replies
5.6k
views
How to get the intersect and get the difference of a grange object while keeping meta data
genomicranges intersect
updated 9.7 years ago by 4.3k • written 9.8 years ago by ▴ 30
0
votes
6
replies
5.6k
views
Package ‘GenomicRanges’ version 1.20.8 cannot be unloaded
rapidr genomicranges
10.3 years ago Pau Marc Muñoz Torres ▴ 20
2
votes
7
replies
5.5k
views
coverage over specific GenomicRanges
genomicranges
updated 10.6 years ago by 16k • written 10.6 years ago by ▴ 90
9
votes
9
replies
5.4k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 10
0
votes
4
replies
5.4k
views
GRanges DitancetoNearest query
Transcription GenomicRanges Transcription GenomicRanges
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ▴ 150
4
votes
4
replies
5.4k
views
How to bin a GRanges to small bins
GenomicRanges
updated 10.1 years ago by ★ 11k • written 10.1 years ago by ▴ 200
9
votes
11
replies
5.4k
views
looping through a GRangesList object
GenomicRanges GRangesList
updated 10.1 years ago by ★ 1.3k • written 10.1 years ago by ★ 3.8k
2
votes
2
replies
5.2k
views
Concatenate a list of genomic ranges
r granges genomicranges
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
4
votes
3
replies
5.2k
views
subsetting GRanges object based on gene IDs
genomicranges genomicfeatures granges subsetting
8.4 years ago Assa Yeroslaviz ★ 1.5k
2
votes
5
replies
5.1k
views
GRanges - add names when constructing a new GRanges, rather than afterwards?
genomicranges
updated 10.4 years ago by ★ 11k • written 10.4 years ago by ▴ 740
7
votes
5
replies
5.1k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 7.3 years ago by • 0 • written 8.4 years ago by ★ 1.5k
1
vote
6
replies
5.0k
views
reduce function in GenomicRanges
genomicranges reduce
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 20
2
votes
4
replies
4.9k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 4.1 years ago by 16k • written 4.3 years ago by ▴ 20
0
votes
6
replies
4.9k
views
GRanges::distanceToNearest does not return distance to nearest
granges genomicranges
updated 8.1 years ago by ★ 6.8k • written 8.2 years ago by ▴ 40
7
votes
0
replies
4.7k
views
Tutorial: New edX "Data analysis for Life Sciences" module: High performance computing for reproducible genomics
annotation genomicranges visualization docker shiny Tutorial
9.9 years ago Vincent J. Carey, Jr. 6.7k
0
votes
5
replies
4.7k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
4.6 years ago rtrivedi1 ▴ 10
1
vote
4
replies
4.7k
views
Generate 3' UTR and 5' UTR ranges from a gff file
gff genomicranges
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 10
4
votes
10
replies
4.5k
views
mapCoords for converting genomic coordinates to cDNA coordinates?
genomicranges
updated 11.3 years ago by ★ 6.8k • written 11.3 years ago by ▴ 10
0
votes
7
replies
4.3k
views
GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
S4Vectors GenomicRanges BiocManager
6.3 years ago james.dalgleish ▴ 30
5
votes
10
replies
4.3k
views
tileGenome for overlapping ranges?
genomicranges
updated 10.5 years ago by • 0 • written 11.0 years ago by ▴ 740
4
votes
5
replies
4.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 2.0 years ago by ▴ 10 • written 10.2 years ago by ▴ 10
3
votes
21
replies
4.2k
views
`precede` does not perform as expected
genomicranges precede ph525.5x
9.1 years ago wcstcyx ▴ 30
0
votes
6
replies
4.1k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster quasR genomicfeatures genomicranges alignment
updated 10.6 years ago by 16k • written 10.6 years ago by ▴ 70
6
votes
8
replies
4.1k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 90
5
votes
8
replies
4.1k
views
Large disk images of DESeqDataSet / SummarizedExperiment objects when using the save function
SummarizedExperiment DESeqDataSet GenomicRanges DESeq2 save
updated 11.0 years ago by ★ 13k • written 11.0 years ago by ▴ 30
3
votes
5
replies
4.0k
views
Element-wise setdiff when psetdiff fails for GenomicRanges
genomicranges iranges genomics
updated 11.1 years ago by ▴ 60 • written 11.1 years ago by ▴ 150
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