Showing : IRanges • reset
1
vote
1
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47
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mean coverage plot of IRanges / Granges object
IRanges
updated 18 days ago by 56k • written 18 days ago by • 0
1
vote
2
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111
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Question about nearest function in R package IRanges
nearest IRanges
updated 7 weeks ago by ★ 4.3k • written 7 weeks ago by • 0
2
votes
3
replies
110
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
4 months ago Nicholas • 0
1
vote
1
reply
133
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 5 months ago by 56k • written 5 months ago by • 0
0
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1
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96
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need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 6 months ago by ▴ 130 • written 11 months ago by • 0
0
votes
1
reply
100
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 7 months ago by 56k • written 7 months ago by ▴ 50
0
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1
reply
99
views
how to plot iranges in r version 4.0.0?
IRanges
9 months ago aissabenyoucef • 0
0
votes
1
reply
96
views
Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4 Rcpp InteractionSet IRanges Rle
updated 10 months ago by ★ 26k • written 10 months ago by • 0
8
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10
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220
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Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges IRanges
updated 10 months ago by 56k • written 10 months ago by ▴ 50
4
votes
6
replies
142
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CAGEr - Error with aggregateTagClusters() - invalid class IRanges object: width(x) cannot contain negative integers
CAGEr IRanges aggregateTagClusters
11 months ago mirkocelii ▴ 40
0
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0
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73
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No methods found in package Biobase for request: read.AnnotatedDataFrame
software error biobase Iranges ArrayExpressHTS
13 months ago Ed Siefker ▴ 230
6
votes
11
replies
2.8k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 14 months ago by • 0 • written 6.1 years ago by ▴ 20
0
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0
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166
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
16 months ago YH • 0
0
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4
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383
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IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges rtracklayer
updated 17 months ago by 56k • written 17 months ago by ▴ 10
0
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0
replies
115
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
17 months ago jovel_juan ▴ 10
0
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1
reply
578
views
Error in IRanges, In range 1: 'end' must be >= 'start' - 1.: .Call2(\"solve_user_SEW0\", start, end, width, PACKAGE = \"IRanges\")"
Genomicranges IRanges
updated 18 months ago by 56k • written 18 months ago by • 0
0
votes
7
replies
258
views
Best way to subset one IRanges by list of IRanges
iranges
19 months ago Robert M. Flight ▴ 280
1
vote
3
replies
340
views
Correct way to split and unsplit a DataFrame
s4vectors iranges
updated 20 months ago by 11k • written 20 months ago by ▴ 70
0
votes
1
reply
203
views
Diffbind problems with negative widths in IRanges and chromosome ranges after dba.report
diffbind IRanges
updated 20 months ago by ★ 3.8k • written 20 months ago by • 0
0
votes
1
reply
220
views
Annotating protein sequences
Protein iranges sequencing
2.1 years ago ieuangw • 0
2
votes
2
replies
731
views
Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 2.3 years ago by ★ 26k • written 2.3 years ago by • 0
4
votes
2
replies
397
views
Speed efficient way to select the n-th element from GRangsList
R GenomicRanges IRanges
2.3 years ago foehn ▴ 60
3
votes
7
replies
4.9k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 2.4 years ago by • 0 • written 5.6 years ago by ▴ 50
2
votes
1
reply
359
views
Bug in follow and precede
software error genomicranges iranges
updated 2.4 years ago by ★ 6.7k • written 2.4 years ago by • 0
0
votes
3
replies
324
views
GenomicRanges based on indices or more conditions, and add column from match
genomicranges iranges findoverlaps
2.5 years ago francesca casalino ▴ 50
2
votes
3
replies
436
views
Gaia results including negative widths
gaia genomicranges iranges
updated 2.7 years ago by ▴ 30 • written 2.7 years ago by ▴ 10
2
votes
1
reply
305
views
IRanges seqselect and subsetByRanges
Iranges defunct
updated 2.7 years ago by 11k • written 2.7 years ago by • 0
0
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15
replies
696
views
Looking for the source for IRanges 2.8.1, S4Vectors 0.12.1 and XVector 0.14.0
bioconductor iranges s4vectors xvector r 3.3.2
updated 2.7 years ago by ▴ 10 • written 2.7 years ago by • 0
0
votes
0
replies
355
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
2.8 years ago kicheol.kim • 0
1
vote
0
replies
1.0k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
2.8 years ago kicheol.kim • 0
0
votes
1
reply
404
views
TEQC - new version Bioc - problem with IRanges
teqc iranges
updated 2.8 years ago by ▴ 10 • written 2.8 years ago by • 0
0
votes
0
replies
316
views
Avoid rotating vector when doing arithmetic on different length IRanges RleList entries
iranges s4vectors rle rlelist
2.8 years ago endrebak85 ▴ 30
2
votes
2
replies
812
views
IRanges which are not S4 generic: endoapply mendoapply error in loading oligoclasses
iranges oligoclasses BiocGenerics
2.8 years ago GENOMIC_region • 0
0
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1
reply
329
views
CNRegions gives error in IRanges Package
CNregions iranges iClusterPlus
2.9 years ago sumonaray55 • 0
0
votes
2
replies
446
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
2.9 years ago Vivek.b ▴ 100
2
votes
5
replies
2.1k
views
unlist doesn't work for IRanges
iranges
updated 2.9 years ago by 56k • written 2.9 years ago by ▴ 450
1
vote
2
replies
464
views
Detecting Overlaps within Grange Object
r grange granges iranges
updated 3.1 years ago by 11k • written 3.1 years ago by • 0
0
votes
5
replies
532
views
HiTC importC not working
HiTC IRanges windows debian
updated 3.1 years ago by ▴ 260 • written 3.1 years ago by • 0
0
votes
1
reply
587
views
Error in .Primitive("c")(<S4 object of class "IRanges">) : could not find symbol "recursive" in environment of the generic function running msa
msa iranges
updated 3.2 years ago by ▴ 250 • written 3.2 years ago by • 0
0
votes
1
reply
441
views
Error in export ifelse from IRanges
iranges ifelse package namespace export
updated 3.3 years ago by 56k • written 3.3 years ago by • 0
2
votes
2
replies
482
views
Packages employing RangedSummarizedExperiment objects
rangedsummarizedexperiment packages granges iranges
updated 3.3 years ago by ★ 26k • written 3.3 years ago by ▴ 60
1
vote
4
replies
1.4k
views
biocLite updating problem with Ubuntu 17.10
ubuntu biocgenerics s4vectors IRanges annotationdbi
updated 3.3 years ago by 25k • written 3.3 years ago by • 0
0
votes
1
reply
480
views
Rcpp adding circular ranges to GRanges object in c++
GRanges circular rcpp IRanges
3.4 years ago hauken_heyken ▴ 80
4
votes
17
replies
1.6k
views
How to construct a valid GRanges object from RCPP and pass back to R
GRanges IRanges RCPP Constructor
updated 3.5 years ago by ▴ 10 • written 3.6 years ago by ▴ 80
0
votes
0
replies
440
views
resize functions causes an error - "could not find function "unsafe.update"
genomicranges iranges resize
3.5 years ago Assa Yeroslaviz ★ 1.5k
7
votes
4
replies
1.0k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 3.5 years ago by 14k • written 3.6 years ago by ▴ 40
6
votes
6
replies
693
views
Implementing fast mathematical and statistical operations on genomic variables in bioconductor
genomicranges biocgenerics rlelist genomicvars iranges
updated 3.6 years ago by 14k • written 3.6 years ago by ▴ 20
0
votes
4
replies
551
views
Problem with IRanges and GenomicRanges
iranges genomicranges
updated 3.6 years ago by 14k • written 3.6 years ago by • 0
1
vote
4
replies
861
views
IRanges (GRanges): Inconsistent behaviour when overlapping ranges of width 0
Iranges granges
updated 3.6 years ago by 14k • written 3.7 years ago by ▴ 40
0
votes
3
replies
859
views
Using IRanges to find gene TSS that overlap a window
iranges R granges
updated 3.7 years ago by • 0 • written 3.7 years ago by ▴ 20
265 results • Page 1 of 6
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Answer: unable to forge custom BSgenome after update by Hervé Pagès 14k
Hi, You need to specify the `circ_seqs` field in your seed file. `forgeBSgenomeDataPkg()` needs to know which sequences are circular …
Comment: How to apply limma-trend or voom to batch corrected single cell data? (non-integ by hainct • 0
Thank you @alun
Comment: EnhancedVolcano plot with colCustom by Neeraja Vegesna ▴ 10
Hi Kevin, It worked once I added `names(keyvals.colour1)[keyvals.colour1 == '#8F8F8F'] <- 'NA'`. ![volcanoplot][1] Thanks a lot for you…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mwong043 • 0
Thanks Rory. I tried the first method by defining a vector containing the normalisation factors for my samples and it worked. I am just wo…
Comment: EnhancedVolcano plot with colCustom by Kevin Blighe 2.8k
Hi, that's great that it works with a lower number of groups. Can you re-check the logic flow when you are using more groups? *EnhancedVolc…
Votes
mgcv not updating
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Comment: EnhancedVolcano plot with colCustom
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