Showing : GenomicRanges • reset
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Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
11 days ago alorsonmethyle • 0
1
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4
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130
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IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
18 days ago • updated 7 days ago Yixin • 0
11
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13
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588
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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 months ago • updated 3 months ago rohitsatyam102 ▴ 10
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1
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133
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cannot create GRanges object anymore
GenomicR GenomicRanges
updated 4 months ago by 56k • written 4 months ago by • 0
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1
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101
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Average coverage between multiple samples
GenomicRanges
updated 5 months ago by 11k • written 5 months ago by ▴ 70
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10
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9.6k
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How do I merge a list of GRanges?
GenomicRanges
updated 3 months ago by ▴ 30 • written 4.9 years ago by ▴ 30
1
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1
reply
149
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GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 5 months ago by 56k • written 5 months ago by • 0
1
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3
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163
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Merging Neighboring Genomic Segments
Granges GenomicRanges
6 months ago • updated 5 months ago rahnaman ▴ 10
2
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2
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208
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How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 6 months ago by 14k • written 7 months ago by ▴ 80
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65
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annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
6 months ago Nala • 0
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0
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105
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Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
7 months ago r.a.policastro • 0
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1
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117
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How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 8 months ago by 56k • written 8 months ago by ▴ 50
3
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7
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244
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GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 9 months ago by 56k • written 9 months ago by ▴ 10
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95
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Expected Output for Promoters Used for GRangesList
GenomicRanges
9 months ago Dario Strbenac ★ 1.5k
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5
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140
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GenomicRanges object no longer viewable
GenomicRanges
updated 11 months ago by 25k • written 11 months ago by ▴ 80
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2
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131
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How to extract positions present in one genomic ranges object and not the other?
genomicranges r overlap
updated 12 months ago by 2.9k • written 12 months ago by • 0
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1
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104
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Is there an easy way to do pos(x) <- pos(x) + 1 for a GPos object ?
GenomicRanges GPos
12 months ago Charles Plessy ▴ 130
0
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0
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107
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A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
12 months ago shangguandong1996 ▴ 20
2
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2
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165
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Genomic Ranges: Convert from 0-base to 1-base
GenomicRanges
updated 12 months ago by 11k • written 12 months ago by ▴ 10
1
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1
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204
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Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 13 months ago by 11k • written 13 months ago by ▴ 20
3
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4
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207
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how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 13 months ago by 14k • written 14 months ago by ▴ 20
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4
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207
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Compilation error when attempting to install GenomicRanges from BiocManager.
software error GenomicRanges
14 months ago atheeth14 • 0
1
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1
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93
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MEDIPS.CpGenrich now that RangedData is deprecated
MEDIPS RangedData GenomicRanges
updated 14 months ago by ▴ 550 • written 14 months ago by • 0
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6
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183
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GenomicRanges: Find first, second and third nearest genes
R GenomicRanges Granges
updated 14 months ago by 42k • written 14 months ago by ▴ 20
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0
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123
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Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 15 months ago by 2.7k • written 15 months ago by • 0
3
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2
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172
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GenomicRanges: Find N nearest/preceding/following ranges
genomicranges
updated 15 months ago by 11k • written 15 months ago by ▴ 140
6
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11
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2.8k
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Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 15 months ago by • 0 • written 6.2 years ago by ▴ 20
2
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3
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133
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GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 16 months ago by 56k • written 16 months ago by ▴ 10
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3
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196
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Resize exons in transcript to total width
genomicranges genomicfeatures
updated 17 months ago by 11k • written 17 months ago by ▴ 70
0
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1
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176
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An error while finding pintersect()
GenomicRanges
18 months ago Prashantha Hebbar ▴ 260
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130
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SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
18 months ago rmash • 0
0
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1
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628
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Error in IRanges, In range 1: 'end' must be >= 'start' - 1.: .Call2(\"solve_user_SEW0\", start, end, width, PACKAGE = \"IRanges\")"
Genomicranges IRanges
updated 19 months ago by 56k • written 19 months ago by • 0
2
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3
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275
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Can GenomicRanges findOverlaps ignore seqnames?
GenomicRanges findOverlaps
19 months ago O. William McClung • 0
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7
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1.2k
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GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
S4Vectors GenomicRanges BiocManager
19 months ago james.dalgleish ▴ 30
4
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9
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308
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Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 20 months ago by 56k • written 20 months ago by • 0
0
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5
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249
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A Problem about seqnames() in GenomicRanges
GenomicRanges
20 months ago shangguandong1996 ▴ 20
0
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3
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316
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Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
20 months ago Aditya ▴ 120
1
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2
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232
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Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 20 months ago by 11k • written 20 months ago by ▴ 120
4
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14
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586
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Subsetting a GenomicRanges::GRanges with "%in%" fails
genomicranges
20 months ago Aditya ▴ 120
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3
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291
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Is range validity checked after GRanges operations?
GenomicRanges
20 months ago Aditya ▴ 120
7
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4
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214
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seqlengths is not an exported object from namespace GenomicRanges
GenomicRanges
updated 20 months ago by 11k • written 20 months ago by ▴ 120
2
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1
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245
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How to make a GPos subclass that accept both UnstitchedGPos and StitchedGPos inputs?
GenomicRanges
updated 21 months ago by 14k • written 22 months ago by ▴ 130
3
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10
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1.6k
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Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
22 months ago Robert ▴ 10
2
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3
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343
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"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 22 months ago by 13k • written 22 months ago by ▴ 30
4
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2
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410
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Build GPos from IPos
genomicranges granges gpos
updated 23 months ago by 14k • written 2.6 years ago by ▴ 140
0
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1
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211
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Assesing genomic segment enrichment with GenomicRanges (R-package)
GenomicRanges R genomic enrichment
updated 23 months ago by 11k • written 23 months ago by • 0
0
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1
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169
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how to remove row which value were found in group before
GenomicRanges r
24 months ago naktang1 • 0
0
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1
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281
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Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 5 days ago by • 0 • written 2.0 years ago by • 0
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2
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282
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calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
2.0 years ago tangming2005 ▴ 160
3
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2
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1.1k
views
invalid class GRanges object: 1: 'x@seqnames' is not parallel to 'x
genomicranges
updated 2.1 years ago by ▴ 80 • written 2.1 years ago by ▴ 10
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Comment: `aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size awa by Koki • 0
Ok, I got the gist of it. If I have the same situation of the previous case (https://support.bioconductor.org/p/9136736/), where I have to…
Answer: DESeq2 Design matrix by Michael Love 33k
Usually one would use a single design and extract comparisons. With a complex design, you should partner with someone familiar with linear …
Comment: `aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size awa by Hervé Pagès 14k
> For example, the following codes use a combination of delayed operation and block-processed operation but the code as a whole does not ex…
Answer: Technical reps by Michael Love 33k
I would go back and attempt to map but allowing a higher insert size. I think a number of RNA-seq alignment tools have this as an option. I…
Comment: ASpli: jCounts() Error in av[at] <- a[at] : NAs are not allowed in subscripted a by Emma ▴ 10
Hi Estefi, I tried to do the devel version install, but it requires R 4.1, which I don't have on my cluster. It's not possible for me to …
Votes
Comment: `aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size awa
Answer: Error: C stack usage of HDF5Array
Answer: "dim<-" against on-disk arrays
Answer: `aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size awa
Answer: ASpli: jCounts() Error in av[at] <- a[at] : NAs are not allowed in subscripted a
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