Showing : Iranges • reset
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63
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Extracting values from out-of-bounds Rle Views
IRanges XVector AtomicList
9 weeks ago Pierre-Luc Germain • 0
1
vote
2
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216
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Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
3 months ago vanbelj ▴ 10
0
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2
replies
294
views
slidingIRanges in IRanges ... odd behavior
IRanges
updated 9 months ago by 15k • written 9 months ago by ▴ 10
1
vote
2
replies
320
views
How to apply a function to a RleViesList object?
Views IRanges GRanges RleList
updated 10 months ago by ★ 5.7k • written 10 months ago by ★ 1.5k
2
votes
3
replies
369
views
how to get genomic coordinates from an MIndex object
IRanges MIndex
updated 12 months ago by 11k • written 12 months ago by ▴ 110
1
vote
4
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588
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
15 months ago Yixin • 0
1
vote
1
reply
287
views
mean coverage plot of IRanges / Granges object
IRanges
updated 16 months ago by 60k • written 16 months ago by • 0
1
vote
2
replies
477
views
Question about nearest function in R package IRanges
nearest IRanges
updated 17 months ago by ★ 4.3k • written 17 months ago by • 0
2
votes
3
replies
421
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
20 months ago Nicholas Cooley • 0
1
vote
1
reply
503
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 21 months ago by 60k • written 21 months ago by • 0
0
votes
1
reply
389
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 23 months ago by 60k • written 23 months ago by ▴ 50
0
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1
reply
310
views
how to plot iranges in r version 4.0.0?
IRanges
2.1 years ago aissabenyoucef • 0
0
votes
1
reply
352
views
Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4 Rcpp InteractionSet IRanges Rle
updated 2.2 years ago by ★ 27k • written 2.2 years ago by • 0
8
votes
10
replies
630
views
Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges IRanges
updated 2.2 years ago by 60k • written 2.2 years ago by ▴ 50
0
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1
reply
333
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 22 months ago by ▴ 140 • written 2.2 years ago by • 0
4
votes
6
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478
views
CAGEr - Error with aggregateTagClusters() - invalid class IRanges object: width(x) cannot contain negative integers
CAGEr IRanges aggregateTagClusters
2.3 years ago mirkocelii ▴ 40
0
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0
replies
322
views
No methods found in package Biobase for request: read.AnnotatedDataFrame
software error biobase Iranges ArrayExpressHTS
2.4 years ago Ed Siefker ▴ 230
0
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0
replies
361
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
2.7 years ago • updated 2.6 years ago YH • 0
0
votes
4
replies
870
views
IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges rtracklayer
updated 2.8 years ago by 60k • written 2.8 years ago by ▴ 10
0
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0
replies
335
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
2.8 years ago jovel_juan ▴ 10
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1
reply
1.3k
views
Error in IRanges, In range 1: 'end' must be >= 'start' - 1.: .Call2(\"solve_user_SEW0\", start, end, width, PACKAGE = \"IRanges\")"
Genomicranges IRanges
updated 2.8 years ago by 60k • written 2.8 years ago by • 0
0
votes
7
replies
692
views
Best way to subset one IRanges by list of IRanges
iranges
2.9 years ago Robert M. Flight ▴ 280
1
vote
3
replies
711
views
Correct way to split and unsplit a DataFrame
s4vectors iranges
updated 3.0 years ago by 11k • written 3.0 years ago by ▴ 70
0
votes
1
reply
376
views
Diffbind problems with negative widths in IRanges and chromosome ranges after dba.report
diffbind IRanges
updated 3.0 years ago by ★ 4.4k • written 3.0 years ago by • 0
0
votes
1
reply
435
views
Annotating protein sequences
Protein iranges sequencing
3.4 years ago ieuangw • 0
2
votes
2
replies
1.1k
views
Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 3.6 years ago by ★ 27k • written 3.6 years ago by • 0
4
votes
2
replies
582
views
Speed efficient way to select the n-th element from GRangsList
R GenomicRanges IRanges
3.7 years ago foehn ▴ 80
2
votes
1
reply
565
views
Bug in follow and precede
software error genomicranges iranges
updated 3.7 years ago by ★ 6.7k • written 3.7 years ago by • 0
0
votes
3
replies
543
views
GenomicRanges based on indices or more conditions, and add column from match
genomicranges iranges findoverlaps
3.8 years ago francesca casalino ▴ 50
3
votes
3
replies
762
views
Gaia results including negative widths
gaia genomicranges iranges
updated 4.0 years ago by ▴ 40 • written 4.0 years ago by ▴ 10
2
votes
1
reply
479
views
IRanges seqselect and subsetByRanges
Iranges defunct
updated 4.0 years ago by 11k • written 4.0 years ago by • 0
0
votes
15
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1.1k
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 4.1 years ago by ▴ 10 • written 4.1 years ago by • 0
0
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0
replies
553
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
4.1 years ago kicheol.kim • 0
1
vote
0
replies
1.5k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
4.1 years ago kicheol.kim • 0
0
votes
0
replies
508
views
Avoid rotating vector when doing arithmetic on different length IRanges RleList entries
iranges s4vectors rle rlelist
4.1 years ago endrebak85 ▴ 30
2
votes
2
replies
1.3k
views
IRanges which are not S4 generic: endoapply mendoapply error in loading oligoclasses
iranges oligoclasses BiocGenerics
4.2 years ago GENOMIC_region • 0
0
votes
1
reply
621
views
TEQC - new version Bioc - problem with IRanges
teqc iranges
updated 4.1 years ago by ▴ 10 • written 4.2 years ago by • 0
0
votes
1
reply
513
views
CNRegions gives error in IRanges Package
CNregions iranges iClusterPlus
4.2 years ago sumonaray55 • 0
0
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2
replies
711
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
4.2 years ago Vivek.b ▴ 100
2
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5
replies
3.3k
views
unlist doesn't work for IRanges
iranges
updated 4.2 years ago by 60k • written 4.2 years ago by ▴ 450
1
vote
2
replies
707
views
Detecting Overlaps within Grange Object
r grange granges iranges
updated 4.4 years ago by 11k • written 4.4 years ago by • 0
0
votes
5
replies
880
views
HiTC importC not working
HiTC IRanges windows debian
updated 4.4 years ago by ▴ 260 • written 4.4 years ago by • 0
0
votes
1
reply
817
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 4.6 years ago by ▴ 290 • written 4.6 years ago by • 0
0
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1
reply
658
views
Error in export ifelse from IRanges
iranges ifelse package namespace export
updated 4.6 years ago by 60k • written 4.6 years ago by • 0
2
votes
2
replies
746
views
Packages employing RangedSummarizedExperiment objects
rangedsummarizedexperiment packages granges iranges
updated 4.6 years ago by ★ 27k • written 4.6 years ago by ▴ 60
1
vote
4
replies
1.9k
views
biocLite updating problem with Ubuntu 17.10
ubuntu biocgenerics s4vectors IRanges annotationdbi
updated 4.7 years ago by 25k • written 4.7 years ago by • 0
0
votes
1
reply
673
views
Rcpp adding circular ranges to GRanges object in c++
GRanges circular rcpp IRanges
4.7 years ago hauken_heyken ▴ 80
0
votes
0
replies
612
views
resize functions causes an error - "could not find function "unsafe.update"
genomicranges iranges resize
4.8 years ago Assa Yeroslaviz ★ 1.5k
7
votes
4
replies
1.4k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 4.9 years ago by 15k • written 4.9 years ago by ▴ 40
6
votes
6
replies
997
views
Implementing fast mathematical and statistical operations on genomic variables in bioconductor
genomicranges biocgenerics rlelist genomicvars iranges
updated 4.9 years ago by 15k • written 4.9 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: Conversion of UniProt to Ensembl by James W. MacDonald 60k
I will provide an example below. But first, there is a vignette for biomaRt (actually two), and it has extensive examples of how to use the…
Comment: the difference between getGEO and getGEOSuppFiles by Fatemeh • 0
thank you!
Answer: the difference between getGEO and getGEOSuppFiles by James W. MacDonald 60k
When submitting data to GEO, you are supposed to provide both the raw data and a matrix of processed data. When you use `getGEO` you get th…
Comment: error running UniProt.ws by James W. MacDonald 60k
https://www.bioconductor.org/checkResults/3.15/bioc-LATEST/UniProt.ws/nebbiolo1-install.html
Comment: error running UniProt.ws by James W. MacDonald 60k
@marcelramos You have introduced a dependency on `BiocBaseUtils`, but that package is only available in devel.
Votes
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
Answer: the difference between getGEO and getGEOSuppFiles
Answer: the difference between getGEO and getGEOSuppFiles
Answer: TPM normalization starting with read counts
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