Showing : GenomicRanges • reset
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How to overlap granges objects by gene name
GenomicRanges
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
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5
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4.7k
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Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
4.7 years ago rtrivedi1 ▴ 10
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Arithmetic Operations Between GRanges' Scores
GenomicRanges
4.7 years ago Dario Strbenac ★ 1.6k
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2
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1.4k
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Should I create a new class or using Common Classes
GenomicRanges
updated 4.8 years ago by 16k • written 4.8 years ago by ▴ 40
1
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4
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2.4k
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IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
4.8 years ago Yixin • 0
11
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13
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7.3k
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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 5.1 years ago rohitsatyam102 ▴ 20
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1.6k
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cannot create GRanges object anymore
GenomicR GenomicRanges
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
1
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1
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1.5k
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Average coverage between multiple samples
GenomicRanges
updated 5.2 years ago by ★ 11k • written 5.2 years ago by ▴ 90
20
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10
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22k
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How do I merge a list of GRanges?
GenomicRanges
updated 4.1 years ago by ▴ 40 • written 9.7 years ago by ▴ 40
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1
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2.1k
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GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
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3
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3.5k
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Merging Neighboring Genomic Segments
Granges GenomicRanges
5.3 years ago rahnaman ▴ 10
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2
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2.4k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 5.3 years ago by 16k • written 5.4 years ago by ▴ 80
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0
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1.3k
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annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
5.3 years ago Nala • 0
0
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1
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2.1k
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How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 50
3
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7
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2.3k
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GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 5.6 years ago by 68k • written 5.6 years ago by ▴ 30
0
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0
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989
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Expected Output for Promoters Used for GRangesList
GenomicRanges
5.6 years ago Dario Strbenac ★ 1.6k
0
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5
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2.5k
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GenomicRanges object no longer viewable
GenomicRanges
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 80
5
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2
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3.1k
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How to extract positions present in one genomic ranges object and not the other?
genomicranges r overlap
updated 5.8 years ago by ★ 4.0k • written 5.8 years ago by • 0
0
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1
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1.1k
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Is there an easy way to do pos(x) <- pos(x) + 1 for a GPos object ?
GenomicRanges GPos
5.8 years ago Charles Plessy ▴ 180
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1.4k
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A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
5.8 years ago Guandong Shang ▴ 40
2
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2
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2.7k
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Genomic Ranges: Convert from 0-base to 1-base
GenomicRanges
updated 5.8 years ago by ★ 11k • written 5.8 years ago by ▴ 10
1
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1
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3.3k
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Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 5.9 years ago by ★ 11k • written 5.9 years ago by ▴ 20
3
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4
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1.7k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 5.9 years ago by 16k • written 5.9 years ago by ▴ 40
0
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4
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3.6k
views
Compilation error when attempting to install GenomicRanges from BiocManager.
software error GenomicRanges
6.0 years ago atheeth14 • 0
1
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1
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1.2k
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MEDIPS.CpGenrich now that RangedData is deprecated
MEDIPS RangedData GenomicRanges
updated 6.0 years ago by ▴ 570 • written 6.0 years ago by • 0
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6
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3.2k
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GenomicRanges: Find first, second and third nearest genes
R GenomicRanges Granges
updated 6.0 years ago by 53k • written 6.0 years ago by ▴ 20
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0
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1.4k
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Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 6.0 years ago by 4.3k • written 6.0 years ago by • 0
3
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2
replies
1.6k
views
GenomicRanges: Find N nearest/preceding/following ranges
genomicranges
updated 6.1 years ago by ★ 11k • written 6.1 years ago by ▴ 180
8
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12
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7.3k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 3.6 years ago by • 0 • written 10.9 years ago by ▴ 20
2
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3
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1.9k
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GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 6.1 years ago by 68k • written 6.1 years ago by ▴ 30
0
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3
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1.4k
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Resize exons in transcript to total width
genomicranges genomicfeatures
updated 6.2 years ago by ★ 11k • written 6.2 years ago by ▴ 90
0
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1
reply
962
views
An error while finding pintersect()
GenomicRanges
6.3 years ago Prashantha Hebbar ▴ 260
2
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0
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1.2k
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SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
6.3 years ago rmash ▴ 20
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1
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3.6k
views
Error in IRanges, In range 1: 'end' must be >= 'start' - 1.: .Call2(\"solve_user_SEW0\", start, end, width, PACKAGE = \"IRanges\")"
Genomicranges IRanges
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
2
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3
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1.7k
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Can GenomicRanges findOverlaps ignore seqnames?
GenomicRanges findOverlaps
6.4 years ago O. William McClung • 0
0
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7
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4.3k
views
GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
S4Vectors GenomicRanges BiocManager
6.4 years ago james.dalgleish ▴ 30
4
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9
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2.6k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
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5
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1.8k
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A Problem about seqnames() in GenomicRanges
GenomicRanges
6.5 years ago Guandong Shang ▴ 40
0
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3
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2.0k
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Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
6.5 years ago Aditya ▴ 160
1
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2
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1.6k
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 6.5 years ago by ★ 11k • written 6.5 years ago by ▴ 160
5
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14
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3.8k
views
Subsetting a GenomicRanges::GRanges with "%in%" fails
genomicranges
6.5 years ago Aditya ▴ 160
3
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3
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1.4k
views
Is range validity checked after GRanges operations?
GenomicRanges
6.5 years ago Aditya ▴ 160
7
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4
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2.3k
views
seqlengths is not an exported object from namespace GenomicRanges
GenomicRanges
updated 6.5 years ago by ★ 11k • written 6.5 years ago by ▴ 160
2
votes
1
reply
889
views
How to make a GPos subclass that accept both UnstitchedGPos and StitchedGPos inputs?
GenomicRanges
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 180
3
votes
10
replies
9.4k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
6.6 years ago Robert ▴ 10
2
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3
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2.4k
views
"Packages required but not available." rtracklayer in OSX is not available to CRAN, resulting in errors for downstream dependencies.
GenomicRanges rtracklayer VariantAnnotation S4Vectors SummarizedExperiment
updated 6.6 years ago by ★ 13k • written 6.6 years ago by ▴ 30
4
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2
replies
1.5k
views
Build GPos from IPos
genomicranges granges gpos
updated 6.7 years ago by 16k • written 7.4 years ago by ▴ 180
0
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1
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1.4k
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Assesing genomic segment enrichment with GenomicRanges (R-package)
GenomicRanges R genomic enrichment
updated 6.7 years ago by ★ 11k • written 6.7 years ago by • 0
0
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1
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763
views
how to remove row which value were found in group before
GenomicRanges r
6.8 years ago naktang1 • 0
0
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1
reply
1.6k
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 4.8 years ago by • 0 • written 6.8 years ago by • 0
406 results • Page 2 of 9
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Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Comment: Deadline Extended: EuroBioC2026 Call for Abstracts by a2a2hset32aa • 0
Attending EuroBioC2026 is an excellent way for researchers to explore the intersection of technology and biology. For those seeking high qu…
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Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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