Showing : GenomicRanges • reset
20
votes
10
replies
21k
views
How do I merge a list of GRanges?
GenomicRanges
updated 3.1 years ago by ▴ 40 • written 8.8 years ago by ▴ 40
17
votes
4
replies
18k
views
How to properly sort GRanges?
granges genomicranges sort seqnames order
updated 10.0 years ago by ▴ 30 • written 10.4 years ago by ▴ 680
9
votes
21
replies
12k
views
annotate GRanges with upstream or downstream nearest gene
GRange genomicranges genomicfeatures
updated 9.2 years ago by ★ 1.3k • written 9.2 years ago by ▴ 200
15
votes
4
replies
12k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 3.0 years ago by 16k • written 8.8 years ago by ▴ 40
17
votes
4
replies
12k
views
How to use GenomicRanges to find overlaps by percentage covered of interval
genomicranges
updated 9.5 years ago by ★ 11k • written 9.5 years ago by ▴ 50
10
votes
3
replies
11k
views
resize (shrink/expand) GenomicRanges
GenomicRanges IRanges
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 40
5
votes
6
replies
10k
views
Merge multiple genomic intervals if overlapping more than xx percents
genomicranges
written 9.8 years ago by ▴ 140
5
votes
8
replies
10k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 3.1 years ago by • 0 • written 9.5 years ago by ▴ 50
0
votes
4
replies
9.3k
views
rtracklayer importing gtf files
rtracklayer DESeq GenomicRanges rtracklayer DESeq GenomicRanges
updated 12.0 years ago by ★ 11k • written 12.0 years ago by ★ 13k
3
votes
10
replies
8.5k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
5.7 years ago Robert ▴ 10
4
votes
1
reply
7.6k
views
how to get genomic coordinates for a list of genes
genomicranges
updated 10.2 years ago by 21k • written 10.2 years ago by ▴ 50
1
vote
3
replies
7.3k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 3.4 years ago by 68k • written 3.4 years ago by ▴ 10
3
votes
4
replies
7.0k
views
Subset GRanges object into new object
R genomicranges subsetting
7.4 years ago jhanks1981 • 0
0
votes
2
replies
7.0k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 11.4 years ago by ★ 11k • written 11.4 years ago by 16k
6
votes
6
replies
6.9k
views
converting a GRangesList object with different lengths into a data frame
genomicranges grangeslist dataframe irangeslist lists
updated 7.5 years ago by ★ 11k • written 7.5 years ago by ★ 1.5k
8
votes
9
replies
6.5k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 9.7 years ago by • 0 • written 9.7 years ago by ★ 1.5k
8
votes
12
replies
6.4k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.7 years ago by • 0 • written 10.0 years ago by ▴ 20
11
votes
0
replies
6.2k
views
Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
9.7 years ago Martin Morgan 25k
5
votes
2
replies
6.1k
views
setdiff for GenomicRanges
genomicranges
updated 8.5 years ago by ★ 11k • written 8.5 years ago by ★ 4.3k
2
votes
8
replies
6.0k
views
GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
genomicranges overlap intersect findoverlaps
7.2 years ago Caroline Grisbach Meissner ▴ 10
3
votes
4
replies
6.0k
views
GenomicRanges: Take union of GRanges and keep metadata?
GRange genomicranges
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 40
1
vote
1
reply
5.7k
views
Error trying to install GenomicRanges
cummerbund rtracklayer genomicranges s4vectors iranges
updated 9.2 years ago by ★ 6.6k • written 9.2 years ago by • 0
11
votes
13
replies
5.6k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
4.3 years ago • updated 4.2 years ago rohitsatyam102 ▴ 20
0
votes
6
replies
5.3k
views
Package ‘GenomicRanges’ version 1.20.8 cannot be unloaded
rapidr genomicranges
9.4 years ago Pau Marc Muñoz Torres ▴ 20
0
votes
2
replies
5.2k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.0 years ago by ▴ 20 • written 3.0 years ago by • 0
6
votes
2
replies
5.2k
views
How to get the intersect and get the difference of a grange object while keeping meta data
genomicranges intersect
updated 8.8 years ago by 4.1k • written 8.9 years ago by ▴ 30
0
votes
4
replies
5.1k
views
GRanges DitancetoNearest query
Transcription GenomicRanges Transcription GenomicRanges
updated 12.6 years ago by ★ 13k • written 12.6 years ago by ▴ 150
4
votes
4
replies
5.0k
views
How to bin a GRanges to small bins
GenomicRanges
updated 9.2 years ago by ★ 11k • written 9.2 years ago by ▴ 200
9
votes
11
replies
4.8k
views
looping through a GRangesList object
GenomicRanges GRangesList
updated 9.2 years ago by ★ 1.3k • written 9.2 years ago by ★ 3.8k
2
votes
2
replies
4.8k
views
Concatenate a list of genomic ranges
r granges genomicranges
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
2
votes
7
replies
4.8k
views
coverage over specific GenomicRanges
genomicranges
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 90
4
votes
3
replies
4.7k
views
subsetting GRanges object based on gene IDs
genomicranges genomicfeatures granges subsetting
7.6 years ago Assa Yeroslaviz ★ 1.5k
7
votes
5
replies
4.6k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 6.4 years ago by • 0 • written 7.5 years ago by ★ 1.5k
2
votes
5
replies
4.6k
views
GRanges - add names when constructing a new GRanges, rather than afterwards?
genomicranges
updated 9.5 years ago by ★ 11k • written 9.5 years ago by ▴ 740
9
votes
9
replies
4.5k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.2 years ago by 68k • written 3.2 years ago by ▴ 10
0
votes
6
replies
4.5k
views
GRanges::distanceToNearest does not return distance to nearest
granges genomicranges
updated 7.3 years ago by ★ 6.8k • written 7.3 years ago by ▴ 40
1
vote
6
replies
4.2k
views
reduce function in GenomicRanges
genomicranges reduce
updated 7.7 years ago by 16k • written 7.7 years ago by ▴ 20
2
votes
4
replies
4.2k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 3.2 years ago by 16k • written 3.4 years ago by ▴ 20
7
votes
0
replies
4.1k
views
Tutorial: New edX "Data analysis for Life Sciences" module: High performance computing for reproducible genomics
annotation genomicranges visualization docker shiny Tutorial
9.0 years ago Vincent J. Carey, Jr. 6.7k
1
vote
4
replies
4.1k
views
Generate 3' UTR and 5' UTR ranges from a gff file
gff genomicranges
updated 7.2 years ago by ★ 11k • written 7.3 years ago by ▴ 10
0
votes
5
replies
4.0k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
3.7 years ago rtrivedi1 ▴ 10
0
votes
7
replies
3.8k
views
GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
S4Vectors GenomicRanges BiocManager
5.5 years ago james.dalgleish ▴ 30
4
votes
5
replies
3.8k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 14 months ago by ▴ 10 • written 9.3 years ago by ▴ 10
4
votes
10
replies
3.7k
views
mapCoords for converting genomic coordinates to cDNA coordinates?
genomicranges
updated 10.4 years ago by ★ 6.8k • written 10.4 years ago by ▴ 10
0
votes
6
replies
3.7k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster quasR genomicfeatures genomicranges alignment
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 70
5
votes
10
replies
3.7k
views
tileGenome for overlapping ranges?
genomicranges
updated 9.6 years ago by • 0 • written 10.1 years ago by ▴ 740
5
votes
8
replies
3.7k
views
Large disk images of DESeqDataSet / SummarizedExperiment objects when using the save function
SummarizedExperiment DESeqDataSet GenomicRanges DESeq2 save
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ▴ 30
1
vote
1
reply
3.6k
views
bedtools like subtract in genomic ranges?
genomicranges
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 90
3
votes
5
replies
3.6k
views
Element-wise setdiff when psetdiff fails for GenomicRanges
genomicranges iranges genomics
updated 10.2 years ago by ▴ 60 • written 10.2 years ago by ▴ 150
3
votes
21
replies
3.5k
views
`precede` does not perform as expected
genomicranges precede ph525.5x
8.2 years ago wcstcyx ▴ 30
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