Showing : genomicranges • reset
3
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2
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1.3k
views
Should I create a new class or using Common Classes
GenomicRanges
updated 4.3 years ago by 16k • written 4.3 years ago by ▴ 40
1
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4
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2.1k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
4.4 years ago • updated 4.3 years ago Yixin • 0
11
votes
13
replies
6.2k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
4.8 years ago • updated 4.6 years ago rohitsatyam102 ▴ 20
1
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1
reply
1.6k
views
cannot create GRanges object anymore
GenomicR GenomicRanges
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
1
vote
1
reply
1.3k
views
Average coverage between multiple samples
GenomicRanges
updated 4.7 years ago by ★ 11k • written 4.7 years ago by ▴ 90
20
votes
10
replies
21k
views
How do I merge a list of GRanges?
GenomicRanges
updated 3.6 years ago by ▴ 40 • written 9.2 years ago by ▴ 40
1
vote
1
reply
1.9k
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
1
vote
3
replies
3.2k
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
4.8 years ago rahnaman ▴ 10
2
votes
2
replies
2.1k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 4.8 years ago by 16k • written 5.0 years ago by ▴ 80
0
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0
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1.2k
views
annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
4.9 years ago Nala • 0
0
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1
reply
1.9k
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 50
3
votes
7
replies
2.1k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 5.1 years ago by 68k • written 5.1 years ago by ▴ 30
0
votes
0
replies
915
views
Expected Output for Promoters Used for GRangesList
GenomicRanges
5.1 years ago Dario Strbenac ★ 1.6k
0
votes
5
replies
2.3k
views
GenomicRanges object no longer viewable
GenomicRanges
updated 5.3 years ago by 25k • written 5.3 years ago by ▴ 80
5
votes
2
replies
2.9k
views
How to extract positions present in one genomic ranges object and not the other?
genomicranges r overlap
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
0
votes
1
reply
982
views
Is there an easy way to do pos(x) <- pos(x) + 1 for a GPos object ?
GenomicRanges GPos
5.3 years ago Charles Plessy ▴ 180
0
votes
0
replies
1.3k
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
5.4 years ago Guandong Shang ▴ 40
2
votes
2
replies
2.2k
views
Genomic Ranges: Convert from 0-base to 1-base
GenomicRanges
updated 5.4 years ago by ★ 11k • written 5.4 years ago by ▴ 10
1
vote
1
reply
3.1k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 5.4 years ago by ★ 11k • written 5.4 years ago by ▴ 20
3
votes
4
replies
1.6k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 5.5 years ago by 16k • written 5.5 years ago by ▴ 40
0
votes
4
replies
3.4k
views
Compilation error when attempting to install GenomicRanges from BiocManager.
software error GenomicRanges
5.5 years ago atheeth14 • 0
1
vote
1
reply
1.0k
views
MEDIPS.CpGenrich now that RangedData is deprecated
MEDIPS RangedData GenomicRanges
updated 5.5 years ago by ▴ 570 • written 5.5 years ago by • 0
0
votes
6
replies
2.9k
views
GenomicRanges: Find first, second and third nearest genes
R GenomicRanges Granges
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 20
0
votes
0
replies
1.3k
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 5.6 years ago by 4.2k • written 5.6 years ago by • 0
3
votes
2
replies
1.4k
views
GenomicRanges: Find N nearest/preceding/following ranges
genomicranges
updated 5.6 years ago by ★ 11k • written 5.6 years ago by ▴ 180
8
votes
12
replies
6.8k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 3.2 years ago by • 0 • written 10.5 years ago by ▴ 20
2
votes
3
replies
1.7k
views
GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 30
0
votes
3
replies
1.2k
views
Resize exons in transcript to total width
genomicranges genomicfeatures
updated 5.7 years ago by ★ 11k • written 5.7 years ago by ▴ 90
0
votes
1
reply
879
views
An error while finding pintersect()
GenomicRanges
5.8 years ago Prashantha Hebbar ▴ 260
2
votes
0
replies
1.1k
views
SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
5.9 years ago rmash ▴ 20
0
votes
1
reply
3.3k
views
Error in IRanges, In range 1: 'end' must be >= 'start' - 1.: .Call2(\"solve_user_SEW0\", start, end, width, PACKAGE = \"IRanges\")"
Genomicranges IRanges
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
2
votes
3
replies
1.5k
views
Can GenomicRanges findOverlaps ignore seqnames?
GenomicRanges findOverlaps
5.9 years ago O. William McClung • 0
0
votes
7
replies
4.1k
views
GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
S4Vectors GenomicRanges BiocManager
5.9 years ago james.dalgleish ▴ 30
4
votes
9
replies
2.2k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
0
votes
5
replies
1.6k
views
A Problem about seqnames() in GenomicRanges
GenomicRanges
6.0 years ago Guandong Shang ▴ 40
0
votes
3
replies
1.8k
views
Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
6.0 years ago Aditya ▴ 160
1
vote
2
replies
1.4k
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 6.0 years ago by ★ 11k • written 6.0 years ago by ▴ 160
5
votes
14
replies
3.4k
views
Subsetting a GenomicRanges::GRanges with "%in%" fails
genomicranges
6.0 years ago Aditya ▴ 160
3
votes
3
replies
1.2k
views
Is range validity checked after GRanges operations?
GenomicRanges
6.0 years ago Aditya ▴ 160
7
votes
4
replies
2.1k
views
seqlengths is not an exported object from namespace GenomicRanges
GenomicRanges
updated 6.0 years ago by ★ 11k • written 6.0 years ago by ▴ 160
2
votes
1
reply
820
views
How to make a GPos subclass that accept both UnstitchedGPos and StitchedGPos inputs?
GenomicRanges
updated 6.1 years ago by 16k • written 6.2 years ago by ▴ 180
3
votes
10
replies
8.9k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
6.2 years ago Robert ▴ 10
2
votes
3
replies
2.1k
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 6.2 years ago by ★ 13k • written 6.2 years ago by ▴ 30
4
votes
2
replies
1.4k
views
Build GPos from IPos
genomicranges granges gpos
updated 6.2 years ago by 16k • written 7.0 years ago by ▴ 180
0
votes
1
reply
1.3k
views
Assesing genomic segment enrichment with GenomicRanges (R-package)
GenomicRanges R genomic enrichment
updated 6.3 years ago by ★ 11k • written 6.3 years ago by • 0
0
votes
1
reply
683
views
how to remove row which value were found in group before
GenomicRanges r
6.3 years ago naktang1 • 0
0
votes
1
reply
1.5k
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 4.3 years ago by • 0 • written 6.3 years ago by • 0
0
votes
2
replies
1.7k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
6.4 years ago tangming2005 ▴ 200
3
votes
2
replies
2.5k
views
invalid class GRanges object: 1: 'x@seqnames' is not parallel to 'x
genomicranges
updated 6.4 years ago by ▴ 80 • written 6.5 years ago by ▴ 10
1
vote
8
replies
1.9k
views
Aggregating scores of multiple metadata columns from one GRanges object on another
GenomicRanges
updated 6.5 years ago by ★ 11k • written 6.5 years ago by • 0
403 results • Page 2 of 9
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Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
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Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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