Showing : Iranges • reset
3
votes
4
replies
905
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 13 months ago by 16k • written 13 months ago by • 0
0
votes
0
replies
466
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
15 months ago Mario Dejung • 0
2
votes
1
reply
1.7k
views
Removing metadata rows containing NA values in GRanges
IRanges GRanges NA
updated 18 months ago by ★ 4.0k • written 18 months ago by • 0
0
votes
3
replies
671
views
Extracting values from out-of-bounds Rle Views
IRanges XVector AtomicList
written 22 months ago by ▴ 20
1
vote
2
replies
1.5k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.0 years ago vanbelj ▴ 30
2
votes
3
replies
1.0k
views
slidingIRanges in IRanges ... odd behavior
IRanges
updated 14 months ago by • 0 • written 2.5 years ago by ▴ 20
1
vote
2
replies
912
views
How to apply a function to a RleViesList object?
Views IRanges GRanges RleList
updated 2.6 years ago by ★ 6.5k • written 2.6 years ago by ★ 1.5k
2
votes
3
replies
1.1k
views
how to get genomic coordinates from an MIndex object
IRanges MIndex
updated 2.7 years ago by ★ 11k • written 2.7 years ago by ▴ 110
1
vote
4
replies
1.4k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
3.0 years ago Yixin • 0
1
vote
1
reply
815
views
mean coverage plot of IRanges / Granges object
IRanges
updated 3.1 years ago by 65k • written 3.1 years ago by • 0
1
vote
2
replies
1.2k
views
Question about nearest function in R package IRanges
nearest IRanges
updated 3.2 years ago by ★ 4.3k • written 3.2 years ago by • 0
2
votes
3
replies
996
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
3.4 years ago Nicholas Cooley • 0
1
vote
1
reply
1.2k
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
0
votes
1
reply
1.1k
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 50
1
vote
2
replies
1.1k
views
how to plot iranges in r version 4.0.0?
IRanges
updated 17 months ago by ▴ 10 • written 3.8 years ago by • 0
0
votes
1
reply
830
views
Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4 Rcpp InteractionSet IRanges Rle
updated 3.9 years ago by ★ 28k • written 3.9 years ago by • 0
8
votes
10
replies
1.9k
views
Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges IRanges
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 50
0
votes
1
reply
879
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 3.5 years ago by ▴ 150 • written 3.9 years ago by • 0
4
votes
6
replies
1.1k
views
CAGEr - Error with aggregateTagClusters() - invalid class IRanges object: width(x) cannot contain negative integers
CAGEr IRanges aggregateTagClusters
4.0 years ago mirkocelii ▴ 40
0
votes
0
replies
871
views
No methods found in package Biobase for request: read.AnnotatedDataFrame
software error biobase Iranges ArrayExpressHTS
4.1 years ago Ed Siefker ▴ 230
0
votes
0
replies
787
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
4.4 years ago • updated 4.3 years ago YH • 0
0
votes
4
replies
1.6k
views
IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges rtracklayer
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 30
0
votes
0
replies
727
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
4.5 years ago jovel_juan ▴ 30
0
votes
1
reply
2.4k
views
Error in IRanges, In range 1: 'end' must be >= 'start' - 1.: .Call2(\"solve_user_SEW0\", start, end, width, PACKAGE = \"IRanges\")"
Genomicranges IRanges
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
0
votes
7
replies
1.6k
views
Best way to subset one IRanges by list of IRanges
iranges
4.6 years ago Robert M. Flight ▴ 280
1
vote
3
replies
1.6k
views
Correct way to split and unsplit a DataFrame
s4vectors iranges
updated 4.7 years ago by ★ 11k • written 4.7 years ago by ▴ 90
0
votes
1
reply
710
views
Diffbind problems with negative widths in IRanges and chromosome ranges after dba.report
diffbind IRanges
updated 4.7 years ago by ★ 5.2k • written 4.7 years ago by • 0
0
votes
1
reply
820
views
Annotating protein sequences
Protein iranges sequencing
5.1 years ago ieuangw • 0
2
votes
2
replies
2.0k
views
Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
4
votes
2
replies
1.1k
views
Speed efficient way to select the n-th element from GRangsList
R GenomicRanges IRanges
5.4 years ago foehn ▴ 100
2
votes
1
reply
1.1k
views
Bug in follow and precede
software error genomicranges iranges
updated 5.4 years ago by ★ 6.8k • written 5.4 years ago by • 0
0
votes
3
replies
1.1k
views
GenomicRanges based on indices or more conditions, and add column from match
genomicranges iranges findoverlaps
5.5 years ago francesca casalino ▴ 50
3
votes
3
replies
1.3k
views
Gaia results including negative widths
gaia genomicranges iranges
updated 5.7 years ago by ▴ 40 • written 5.7 years ago by ▴ 10
2
votes
1
reply
855
views
IRanges seqselect and subsetByRanges
Iranges defunct
updated 5.7 years ago by ★ 11k • written 5.7 years ago by • 0
0
votes
15
replies
2.0k
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 5.8 years ago by ▴ 10 • written 5.8 years ago by • 0
0
votes
0
replies
958
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
5.8 years ago kicheol.kim • 0
1
vote
0
replies
2.0k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
5.8 years ago kicheol.kim • 0
0
votes
0
replies
958
views
Avoid rotating vector when doing arithmetic on different length IRanges RleList entries
iranges s4vectors rle rlelist
5.8 years ago endrebak85 ▴ 40
2
votes
2
replies
1.9k
views
IRanges which are not S4 generic: endoapply mendoapply error in loading oligoclasses
iranges oligoclasses BiocGenerics
5.9 years ago • updated 5.8 years ago GENOMIC_region • 0
0
votes
1
reply
1.1k
views
TEQC - new version Bioc - problem with IRanges
teqc iranges
updated 5.8 years ago by ▴ 10 • written 5.9 years ago by • 0
0
votes
1
reply
956
views
CNRegions gives error in IRanges Package
CNregions iranges iClusterPlus
5.9 years ago sumonaray55 • 0
0
votes
2
replies
1.2k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
5.9 years ago Vivek.b ▴ 100
2
votes
5
replies
4.9k
views
unlist doesn't work for IRanges
iranges
updated 5.9 years ago by 65k • written 5.9 years ago by ▴ 450
1
vote
2
replies
1.4k
views
Detecting Overlaps within Grange Object
r grange granges iranges
updated 6.1 years ago by ★ 11k • written 6.1 years ago by • 0
0
votes
5
replies
1.6k
views
HiTC importC not working
HiTC IRanges windows debian
updated 6.1 years ago by ▴ 260 • written 6.1 years ago by • 0
0
votes
1
reply
1.3k
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 6.3 years ago by ▴ 290 • written 6.3 years ago by • 0
0
votes
1
reply
1.2k
views
Error in export ifelse from IRanges
iranges ifelse package namespace export
updated 6.3 years ago by 65k • written 6.3 years ago by • 0
2
votes
2
replies
1.3k
views
Packages employing RangedSummarizedExperiment objects
rangedsummarizedexperiment packages granges iranges
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 60
1
vote
4
replies
2.5k
views
biocLite updating problem with Ubuntu 17.10
ubuntu biocgenerics s4vectors IRanges annotationdbi
updated 6.4 years ago by 25k • written 6.4 years ago by • 0
0
votes
1
reply
1.0k
views
Rcpp adding circular ranges to GRanges object in c++
GRanges circular rcpp IRanges
6.4 years ago hauken_heyken ▴ 80
50 results • Page 1 of 1
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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