Showing : iranges • reset
1
vote
4
replies
833
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 6 months ago by • 0
3
votes
4
replies
1.6k
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 2.1 years ago by 16k • written 2.1 years ago by • 0
0
votes
0
replies
806
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
2.3 years ago Mario Dejung • 0
1
vote
2
replies
1.5k
views
how to plot iranges in r version 4.0.0?
IRanges
updated 2.5 years ago by ▴ 10 • written 4.9 years ago by • 0
2
votes
1
reply
2.7k
views
Removing metadata rows containing NA values in GRanges
IRanges GRanges NA
updated 2.6 years ago by ★ 4.8k • written 2.6 years ago by • 0
1
vote
2
replies
1.4k
views
IRanges vignette code comment
iranges
updated 2.9 years ago by • 0 • written 10.2 years ago by 43k
0
votes
3
replies
936
views
Extracting values from out-of-bounds Rle Views
IRanges XVector AtomicList
written 2.9 years ago by ▴ 20
1
vote
2
replies
2.2k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
3.0 years ago vanbelj ▴ 30
2
votes
3
replies
1.4k
views
slidingIRanges in IRanges ... odd behavior
IRanges
updated 2.2 years ago by • 0 • written 3.5 years ago by ▴ 20
1
vote
2
replies
1.2k
views
How to apply a function to a RleViesList object?
Views IRanges GRanges RleList
updated 3.6 years ago by ★ 6.6k • written 3.6 years ago by ★ 1.5k
2
votes
3
replies
1.6k
views
how to get genomic coordinates from an MIndex object
IRanges MIndex
updated 3.7 years ago by ★ 11k • written 3.7 years ago by ▴ 110
1
vote
4
replies
2.0k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
4.0 years ago Yixin • 0
1
vote
1
reply
1.1k
views
mean coverage plot of IRanges / Granges object
IRanges
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
1
vote
2
replies
1.6k
views
Question about nearest function in R package IRanges
nearest IRanges
updated 4.2 years ago by ★ 4.3k • written 4.2 years ago by • 0
2
votes
3
replies
1.4k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
4.4 years ago Nicholas Cooley • 0
1
vote
1
reply
1.8k
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
0
votes
1
reply
1.3k
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 4.5 years ago by ▴ 150 • written 5.0 years ago by • 0
0
votes
1
reply
1.7k
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 4.7 years ago by 68k • written 4.7 years ago by ▴ 50
0
votes
1
reply
1.3k
views
Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4 Rcpp InteractionSet IRanges Rle
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
8
votes
10
replies
2.8k
views
Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges IRanges
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 50
4
votes
6
replies
1.6k
views
CAGEr - Error with aggregateTagClusters() - invalid class IRanges object: width(x) cannot contain negative integers
CAGEr IRanges aggregateTagClusters
5.0 years ago mirkocelii ▴ 40
0
votes
0
replies
1.1k
views
No methods found in package Biobase for request: read.AnnotatedDataFrame
software error biobase Iranges ArrayExpressHTS
5.2 years ago Ed Siefker ▴ 230
8
votes
12
replies
6.6k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.8 years ago by • 0 • written 10.1 years ago by ▴ 20
0
votes
0
replies
1.1k
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
5.4 years ago YH • 0
0
votes
4
replies
2.1k
views
IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges rtracklayer
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 30
0
votes
0
replies
944
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
5.5 years ago jovel_juan ▴ 30
0
votes
1
reply
3.1k
views
Error in IRanges, In range 1: 'end' must be >= 'start' - 1.: .Call2(\"solve_user_SEW0\", start, end, width, PACKAGE = \"IRanges\")"
Genomicranges IRanges
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
votes
7
replies
2.2k
views
Best way to subset one IRanges by list of IRanges
iranges
5.6 years ago Robert M. Flight ▴ 280
1
vote
3
replies
2.2k
views
Correct way to split and unsplit a DataFrame
s4vectors iranges
updated 5.7 years ago by ★ 11k • written 5.7 years ago by ▴ 90
0
votes
1
reply
933
views
Diffbind problems with negative widths in IRanges and chromosome ranges after dba.report
diffbind IRanges
updated 5.7 years ago by ★ 5.2k • written 5.7 years ago by • 0
0
votes
1
reply
1.1k
views
Annotating protein sequences
Protein iranges sequencing
6.1 years ago ieuangw • 0
2
votes
2
replies
2.6k
views
Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
4
votes
2
replies
1.4k
views
Speed efficient way to select the n-th element from GRangsList
R GenomicRanges IRanges
6.4 years ago foehn ▴ 100
5
votes
8
replies
10k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 3.2 years ago by • 0 • written 9.6 years ago by ▴ 50
2
votes
1
reply
1.3k
views
Bug in follow and precede
software error genomicranges iranges
updated 6.4 years ago by ★ 6.8k • written 6.4 years ago by • 0
0
votes
3
replies
1.5k
views
GenomicRanges based on indices or more conditions, and add column from match
genomicranges iranges findoverlaps
6.6 years ago francesca casalino ▴ 50
3
votes
3
replies
1.7k
views
Gaia results including negative widths
gaia genomicranges iranges
updated 6.7 years ago by ▴ 40 • written 6.7 years ago by ▴ 10
2
votes
1
reply
1.1k
views
IRanges seqselect and subsetByRanges
Iranges defunct
updated 6.7 years ago by ★ 11k • written 6.8 years ago by • 0
0
votes
15
replies
2.7k
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 6.8 years ago by ▴ 10 • written 6.8 years ago by • 0
0
votes
0
replies
1.2k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.8 years ago kicheol.kim • 0
1
vote
0
replies
2.3k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.8 years ago kicheol.kim • 0
0
votes
1
reply
1.3k
views
TEQC - new version Bioc - problem with IRanges
teqc iranges
updated 6.8 years ago by ▴ 10 • written 6.9 years ago by • 0
0
votes
0
replies
1.2k
views
Avoid rotating vector when doing arithmetic on different length IRanges RleList entries
iranges s4vectors rle rlelist
6.9 years ago endrebak85 ▴ 40
2
votes
2
replies
2.4k
views
IRanges which are not S4 generic: endoapply mendoapply error in loading oligoclasses
iranges oligoclasses BiocGenerics
6.9 years ago GENOMIC_region • 0
0
votes
1
reply
1.3k
views
CNRegions gives error in IRanges Package
CNregions iranges iClusterPlus
6.9 years ago sumonaray55 • 0
0
votes
2
replies
1.5k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
6.9 years ago Vivek.b ▴ 100
2
votes
5
replies
5.8k
views
unlist doesn't work for IRanges
iranges
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 450
1
vote
2
replies
2.1k
views
Detecting Overlaps within Grange Object
r grange granges iranges
updated 7.1 years ago by ★ 11k • written 7.1 years ago by • 0
0
votes
5
replies
2.0k
views
HiTC importC not working
HiTC IRanges windows debian
updated 7.2 years ago by ▴ 260 • written 7.2 years ago by • 0
0
votes
1
reply
1.7k
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 7.3 years ago by ▴ 300 • written 7.3 years ago by • 0
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Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an by James W. MacDonald 68k
Have you figured out how to do this using tidy grammar? Using non-tidy grammar is quite simple, and perhaps you already know how to do that…
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You show how you modified the container, but not how you are running it, which is the critical part.
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your reply. > Per sample all counts are scaled by the same size factor so I strongly assume that something was parsed here …
Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k
Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…
Votes
Answer: How to combine two DESeq2 objects (dds) for analysis
How to combine two DESeq2 objects (dds) for analysis
How can I correctly use phyloseq with Docker?
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
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