Showing : Iranges • reset
1
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4
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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
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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
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803
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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 2.4 years ago by ▴ 10 • written 4.8 years ago by • 0
2
votes
1
reply
2.6k
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
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2
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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
934
views
Extracting values from out-of-bounds Rle Views
IRanges XVector AtomicList
written 2.9 years ago by ▴ 20
1
vote
2
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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
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4
replies
2.0k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
4.0 years ago Yixin • 0
1
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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
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2
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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 4.9 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
5.1 years ago Ed Siefker ▴ 230
8
votes
12
replies
6.5k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.8 years ago by • 0 • written 10.1 years ago by ▴ 20
0
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0
replies
1.1k
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
5.4 years ago • updated 5.3 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
943
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
931
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
6.5 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
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1
reply
1.1k
views
IRanges seqselect and subsetByRanges
Iranges defunct
updated 6.7 years ago by ★ 11k • written 6.7 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
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1
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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
6.8 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
5.7k
views
unlist doesn't work for IRanges
iranges
updated 6.9 years ago by 68k • written 6.9 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 7.1 years ago by ▴ 260 • written 7.1 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
50 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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