Showing : IRanges • reset
1
vote
4
replies
680
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 12 weeks ago by • 0
3
votes
4
replies
1.4k
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 22 months ago by 16k • written 22 months ago by • 0
0
votes
0
replies
733
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
2.0 years ago Mario Dejung • 0
1
vote
2
replies
1.4k
views
how to plot iranges in r version 4.0.0?
IRanges
updated 2.2 years ago by ▴ 10 • written 4.6 years ago by • 0
2
votes
1
reply
2.4k
views
Removing metadata rows containing NA values in GRanges
IRanges GRanges NA
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by • 0
1
vote
2
replies
1.3k
views
IRanges vignette code comment
iranges
updated 2.6 years ago by • 0 • written 9.9 years ago by 43k
0
votes
3
replies
873
views
Extracting values from out-of-bounds Rle Views
IRanges XVector AtomicList
written 2.6 years ago by ▴ 20
1
vote
2
replies
2.0k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.8 years ago vanbelj ▴ 30
2
votes
3
replies
1.3k
views
slidingIRanges in IRanges ... odd behavior
IRanges
updated 23 months ago by • 0 • written 3.2 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 3.3 years ago by ★ 6.6k • written 3.3 years ago by ★ 1.5k
2
votes
3
replies
1.5k
views
how to get genomic coordinates from an MIndex object
IRanges MIndex
updated 3.5 years ago by ★ 11k • written 3.5 years ago by ▴ 110
1
vote
4
replies
1.8k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
3.7 years ago Yixin • 0
1
vote
1
reply
1.0k
views
mean coverage plot of IRanges / Granges object
IRanges
updated 3.8 years ago by 67k • written 3.8 years ago by • 0
1
vote
2
replies
1.5k
views
Question about nearest function in R package IRanges
nearest IRanges
updated 3.9 years ago by ★ 4.3k • written 3.9 years ago by • 0
2
votes
3
replies
1.3k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
4.1 years ago Nicholas Cooley • 0
1
vote
1
reply
1.7k
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 4.2 years ago by 67k • written 4.2 years ago by • 0
0
votes
1
reply
1.2k
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 4.3 years ago by ▴ 150 • written 4.7 years ago by • 0
0
votes
1
reply
1.4k
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 4.4 years ago by 67k • written 4.4 years ago by ▴ 50
0
votes
1
reply
1.2k
views
Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4 Rcpp InteractionSet IRanges Rle
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
8
votes
10
replies
2.5k
views
Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges IRanges
updated 4.6 years ago by 67k • written 4.6 years ago by ▴ 50
4
votes
6
replies
1.5k
views
CAGEr - Error with aggregateTagClusters() - invalid class IRanges object: width(x) cannot contain negative integers
CAGEr IRanges aggregateTagClusters
4.7 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
4.9 years ago Ed Siefker ▴ 230
8
votes
12
replies
6.2k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.5 years ago by • 0 • written 9.8 years ago by ▴ 20
0
votes
0
replies
1.0k
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
5.1 years ago YH • 0
0
votes
4
replies
2.0k
views
IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges rtracklayer
updated 5.2 years ago by 67k • written 5.2 years ago by ▴ 30
0
votes
0
replies
893
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
5.2 years ago jovel_juan ▴ 30
0
votes
1
reply
2.9k
views
Error in IRanges, In range 1: 'end' must be >= 'start' - 1.: .Call2(\"solve_user_SEW0\", start, end, width, PACKAGE = \"IRanges\")"
Genomicranges IRanges
updated 5.3 years ago by 67k • written 5.3 years ago by • 0
0
votes
7
replies
2.0k
views
Best way to subset one IRanges by list of IRanges
iranges
5.3 years ago Robert M. Flight ▴ 280
1
vote
3
replies
2.0k
views
Correct way to split and unsplit a DataFrame
s4vectors iranges
updated 5.4 years ago by ★ 11k • written 5.4 years ago by ▴ 90
0
votes
1
reply
879
views
Diffbind problems with negative widths in IRanges and chromosome ranges after dba.report
diffbind IRanges
updated 5.4 years ago by ★ 5.2k • written 5.5 years ago by • 0
0
votes
1
reply
997
views
Annotating protein sequences
Protein iranges sequencing
5.8 years ago ieuangw • 0
2
votes
2
replies
2.4k
views
Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
4
votes
2
replies
1.3k
views
Speed efficient way to select the n-th element from GRangsList
R GenomicRanges IRanges
6.1 years ago foehn ▴ 100
5
votes
8
replies
9.9k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 2.9 years ago by • 0 • written 9.3 years ago by ▴ 50
2
votes
1
reply
1.3k
views
Bug in follow and precede
software error genomicranges iranges
updated 6.1 years ago by ★ 6.8k • written 6.2 years ago by • 0
0
votes
3
replies
1.4k
views
GenomicRanges based on indices or more conditions, and add column from match
genomicranges iranges findoverlaps
6.3 years ago francesca casalino ▴ 50
3
votes
3
replies
1.6k
views
Gaia results including negative widths
gaia genomicranges iranges
updated 6.5 years ago by ▴ 40 • written 6.5 years ago by ▴ 10
2
votes
1
reply
1.0k
views
IRanges seqselect and subsetByRanges
Iranges defunct
updated 6.5 years ago by ★ 11k • written 6.5 years ago by • 0
0
votes
15
replies
2.5k
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 6.5 years ago by ▴ 10 • written 6.5 years ago by • 0
0
votes
0
replies
1.1k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.5 years ago kicheol.kim • 0
1
vote
0
replies
2.2k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.5 years ago kicheol.kim • 0
0
votes
1
reply
1.3k
views
TEQC - new version Bioc - problem with IRanges
teqc iranges
updated 6.6 years ago by ▴ 10 • written 6.6 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
6.6 years ago endrebak85 ▴ 40
2
votes
2
replies
2.3k
views
IRanges which are not S4 generic: endoapply mendoapply error in loading oligoclasses
iranges oligoclasses BiocGenerics
6.6 years ago GENOMIC_region • 0
0
votes
1
reply
1.2k
views
CNRegions gives error in IRanges Package
CNregions iranges iClusterPlus
6.6 years ago sumonaray55 • 0
0
votes
2
replies
1.5k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
6.7 years ago • updated 6.6 years ago Vivek.b ▴ 100
2
votes
5
replies
5.5k
views
unlist doesn't work for IRanges
iranges
updated 6.7 years ago by 67k • written 6.7 years ago by ▴ 450
1
vote
2
replies
1.8k
views
Detecting Overlaps within Grange Object
r grange granges iranges
updated 6.8 years ago by ★ 11k • written 6.8 years ago by • 0
0
votes
5
replies
1.8k
views
HiTC importC not working
HiTC IRanges windows debian
updated 6.9 years ago by ▴ 260 • written 6.9 years ago by • 0
0
votes
1
reply
1.6k
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 7.0 years ago by ▴ 300 • written 7.0 years ago by • 0
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Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Comment: EdgeR Biological CVs by James • 0
Thank you Gordon and Joseph. I presume question (1) would be answered by using a prior G0 of 0? For question (2), I was expecting a biolog…
Answer: EdgeR Biological CVs by Gordon Smyth 52k
I think your questions are answered by the published paper. You might also like to consult recent papers on edgeR by Yunshun Chen and Pedro…
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How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
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