Showing : GenomicRanges • reset
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Unique GPos taking into account mcols
GenomicRanges unique GPos
15 hours ago maltethodberg ▴ 140
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1
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52
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How to overlap granges objects by gene name
GenomicRanges
updated 10 days ago by 57k • written 10 days ago by • 0
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5
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172
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Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
26 days ago rtrivedi1 ▴ 10
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80
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Arithmetic Operations Between GRanges' Scores
GenomicRanges
5 weeks ago Dario Strbenac ★ 1.5k
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2
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132
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Should I create a new class or using Common Classes
GenomicRanges
updated 9 weeks ago by 15k • written 9 weeks ago by ▴ 20
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78
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Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
11 weeks ago alorsonmethyle • 0
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4
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208
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IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
12 weeks ago • updated 11 weeks ago Yixin • 0
11
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13
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728
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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
8 months ago • updated 5 months ago rohitsatyam102 ▴ 10
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1
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211
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cannot create GRanges object anymore
GenomicR GenomicRanges
updated 6 months ago by 57k • written 6 months ago by • 0
1
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1
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136
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Average coverage between multiple samples
GenomicRanges
updated 7 months ago by 11k • written 7 months ago by ▴ 90
14
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10
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9.9k
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How do I merge a list of GRanges?
GenomicRanges
updated 5 months ago by ▴ 30 • written 5.1 years ago by ▴ 30
1
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1
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192
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GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 8 months ago by 57k • written 8 months ago by • 0
1
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3
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215
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Merging Neighboring Genomic Segments
Granges GenomicRanges
8 months ago rahnaman ▴ 10
2
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2
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279
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How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 8 months ago by 15k • written 10 months ago by ▴ 80
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0
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99
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annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
9 months ago Nala • 0
0
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0
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141
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Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
9 months ago r.a.policastro • 0
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1
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164
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How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 11 months ago by 57k • written 11 months ago by ▴ 50
3
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7
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315
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GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 11 months ago by 57k • written 11 months ago by ▴ 10
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0
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129
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Expected Output for Promoters Used for GRangesList
GenomicRanges
12 months ago Dario Strbenac ★ 1.5k
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5
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189
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GenomicRanges object no longer viewable
GenomicRanges
updated 13 months ago by 25k • written 13 months ago by ▴ 80
4
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2
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172
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How to extract positions present in one genomic ranges object and not the other?
genomicranges r overlap
updated 14 months ago by 3.2k • written 14 months ago by • 0
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1
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146
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Is there an easy way to do pos(x) <- pos(x) + 1 for a GPos object ?
GenomicRanges GPos
14 months ago Charles Plessy ▴ 130
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152
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A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
15 months ago Guandong Shang ▴ 20
2
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2
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212
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Genomic Ranges: Convert from 0-base to 1-base
GenomicRanges
updated 15 months ago by 11k • written 15 months ago by ▴ 10
1
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1
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272
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Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 15 months ago by 11k • written 15 months ago by ▴ 20
3
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4
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268
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how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 16 months ago by 15k • written 16 months ago by ▴ 20
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4
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368
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Compilation error when attempting to install GenomicRanges from BiocManager.
software error GenomicRanges
17 months ago atheeth14 • 0
1
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1
reply
142
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MEDIPS.CpGenrich now that RangedData is deprecated
MEDIPS RangedData GenomicRanges
updated 17 months ago by ▴ 550 • written 17 months ago by • 0
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6
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245
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GenomicRanges: Find first, second and third nearest genes
R GenomicRanges Granges
updated 17 months ago by 43k • written 17 months ago by ▴ 20
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0
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155
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Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 17 months ago by 2.8k • written 17 months ago by • 0
3
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2
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217
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GenomicRanges: Find N nearest/preceding/following ranges
genomicranges
updated 18 months ago by 11k • written 18 months ago by ▴ 140
6
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11
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3.0k
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Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 18 months ago by • 0 • written 6.3 years ago by ▴ 20
2
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3
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169
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GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 18 months ago by 57k • written 18 months ago by ▴ 10
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3
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258
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Resize exons in transcript to total width
genomicranges genomicfeatures
updated 19 months ago by 11k • written 19 months ago by ▴ 90
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1
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218
views
An error while finding pintersect()
GenomicRanges
20 months ago Prashantha Hebbar ▴ 260
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0
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164
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SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
20 months ago rmash • 0
0
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1
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757
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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 21 months ago by 57k • written 21 months ago by • 0
2
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3
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351
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Can GenomicRanges findOverlaps ignore seqnames?
GenomicRanges findOverlaps
21 months ago O. William McClung • 0
0
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7
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1.4k
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GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
S4Vectors GenomicRanges BiocManager
22 months ago james.dalgleish ▴ 30
4
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9
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371
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Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 22 months ago by 57k • written 22 months ago by • 0
0
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5
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298
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A Problem about seqnames() in GenomicRanges
GenomicRanges
22 months ago Guandong Shang ▴ 20
0
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3
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388
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Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
22 months ago Aditya ▴ 120
1
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2
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281
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Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 23 months ago by 11k • written 23 months ago by ▴ 120
4
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14
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726
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Subsetting a GenomicRanges::GRanges with "%in%" fails
genomicranges
23 months ago Aditya ▴ 120
3
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3
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351
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Is range validity checked after GRanges operations?
GenomicRanges
23 months ago Aditya ▴ 120
7
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4
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291
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seqlengths is not an exported object from namespace GenomicRanges
GenomicRanges
updated 23 months ago by 11k • written 23 months ago by ▴ 120
2
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1
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286
views
How to make a GPos subclass that accept both UnstitchedGPos and StitchedGPos inputs?
GenomicRanges
updated 24 months ago by 15k • written 2.0 years ago by ▴ 130
3
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10
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1.8k
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Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
2.1 years ago • updated 2.0 years ago Robert ▴ 10
2
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3
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418
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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 2.0 years ago by 13k • written 2.0 years ago by ▴ 30
4
votes
2
replies
461
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Build GPos from IPos
genomicranges granges gpos
updated 2.1 years ago by 15k • written 2.8 years ago by ▴ 140
50 results • Page 1 of 1
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Comment: DESeq2 question: why I got discrepancy results for DEGs when using different way by Ming ▴ 350
Thx for the advice about the reference levels, in which I did do as you suggested! In fact, I even tried more options just want to see why…
Answer: Time series DE gene analysis with edgeR where specific timepoints have NA levels by Gordon Smyth 43k
> is there a way to incorporate also the information of the additional samples that lack any of the aforementioned levels? NA values are n…
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels by James W. MacDonald 57k
The `voomLmFit` function will automatically fit a linear mixed model accounting for within-subject correlations if you block on patient, so…
Comment: error in getBM (biomaRt): "error: no such table: metadata" by Mike Smith ★ 5.0k
Thanks for providing this solution. Anyone else encountering the issue can test if the cache is a problem by running `getBM()` with the ar…
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels by svlachavas ▴ 780
Dear James, thank you very much for your comment; please excuse me for my naïve additional question, but is there an example in the edgeR …
Votes
tximeta error in fetching genome info
Answer: error in getBM (biomaRt): "error: no such table: metadata"
C: DESeq2 design formula: single control for multiple conditions [RIP-seq]
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Answer: cannot install edgeR on M1 Mac
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