Showing : iranges • reset
17
votes
5
replies
4.1k
views
Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
IRanges
updated 7.1 years ago by 25k • written 7.1 years ago by ▴ 20
10
votes
3
replies
9.3k
views
resize (shrink/expand) GenomicRanges
GenomicRanges IRanges
updated 8.2 years ago by 16k • written 8.2 years ago by ▴ 40
8
votes
12
replies
5.5k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 21 months ago by • 0 • written 9.1 years ago by ▴ 20
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
7
votes
4
replies
2.1k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 40
6
votes
3
replies
2.4k
views
how does coverage() works
biostrings coverage rle iranges
7.9 years ago likeeatingpizza ▴ 10
6
votes
6
replies
1.5k
views
Implementing fast mathematical and statistical operations on genomic variables in bioconductor
genomicranges biocgenerics rlelist genomicvars iranges
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 20
5
votes
2
replies
1.3k
views
Using GRanges and IRanges to simply get all chromosome data
GRanges IRanges
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 30
5
votes
5
replies
1.4k
views
How to extract out wanted IntegerList more elegantly from nested list?
r s4vectors integerlist iranges
updated 7.6 years ago by ★ 11k • written 7.6 years ago by • 0
5
votes
8
replies
8.7k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 2.2 years ago by • 0 • written 8.6 years ago by ▴ 50
5
votes
8
replies
2.2k
views
closest-features equivalent in Bioconductor for finding closest gene(s)
genomicranges granges iranges annotatepeak
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ▴ 80
4
votes
2
replies
1.3k
views
trying to annotate overlaps with external file information
iranges granges
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 50
4
votes
1
reply
995
views
IRanges, Partitioning by End function not found.
IRanges Biostrings
updated 8.3 years ago by 25k • written 8.3 years ago by ▴ 30
4
votes
3
replies
2.1k
views
Overlap the snps
overlap snps granges iranges
updated 9.6 years ago by ★ 11k • written 9.6 years ago by ▴ 10
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
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
4
votes
2
replies
3.2k
views
extracting distance from Hits object
genomicranges iranges
updated 9.3 years ago by 16k • written 9.3 years ago by ▴ 140
4
votes
3
replies
1.1k
views
stacking (partially or completely overlapping) GRanges/IRanges
granges iranges rnaseq
updated 9.2 years ago by 25k • written 9.2 years ago by ★ 2.0k
4
votes
7
replies
2.1k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 20
4
votes
2
replies
1.5k
views
How to find particular types of overlap with GenomicRanges
r genomicranges iranges
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ▴ 50
4
votes
17
replies
3.2k
views
How to construct a valid GRanges object from RCPP and pass back to R
GRanges IRanges RCPP Constructor
updated 6.5 years ago by ▴ 10 • written 6.6 years ago by ▴ 80
3
votes
3
replies
1.1k
views
Find hits of subject that start somewhere in the query by using GRanges / IRanges and findOverlap()
IRanges GRanges findoverlaps R
updated 7.7 years ago by ★ 11k • written 7.7 years ago by • 0
3
votes
5
replies
1.0k
views
IRanges start bigger than end
iranges
8.2 years ago vedran.franke • 0
3
votes
5
replies
1.3k
views
Problem with svn_time() function on IRanges package - trying to run "exomePeak" package
iranges
8.6 years ago m.ghanatbari • 0
3
votes
4
replies
1.7k
views
Introns at transcript expression level
genomicfeatures iranges
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 20
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
3
votes
5
replies
3.1k
views
Element-wise setdiff when psetdiff fails for GenomicRanges
genomicranges iranges genomics
updated 9.3 years ago by ▴ 60 • written 9.3 years ago by ▴ 150
3
votes
2
replies
5.9k
views
get promoter regions (bed format) of genes hg19
IRanges IRanges
updated 10.3 years ago by ★ 6.8k • written 10.3 years ago by ★ 13k
3
votes
4
replies
903
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 13 months ago by 16k • written 13 months ago by • 0
2
votes
1
reply
931
views
Question about parallel manipulation on CharacterList objects
s4vectors IRanges
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 450
2
votes
2
replies
1.2k
views
How to coerce CompressedIntegerList as vector?
s4 coercion iranges integerlist
7.7 years ago jian_liangli • 0
2
votes
2
replies
1.1k
views
How to detect and replace zero index in IntegerList ?
iranges integerlist s4
7.7 years ago Jurat Shahidin ▴ 80
2
votes
4
replies
1.2k
views
How to remove duplicated overlap hit index in IntegerList efficiently [solved] ?
r iranges integerlist
7.6 years ago • updated 7.5 years ago Jurat Shahidin ▴ 80
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
2
votes
2
replies
1.2k
views
How to conditionally combine IntegerList in the DataFrame more elegantly?
r iranges integerlist DataFrame
updated 7.5 years ago by ▴ 80 • written 7.5 years ago by • 0
2
votes
3
replies
995
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
3.4 years ago Nicholas Cooley • 0
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
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
2
votes
6
replies
2.8k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 30
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
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
2
votes
1
reply
1.2k
views
Bioconductor utility with novel projects
Granges IRanges gff import.gff3 strand
updated 9.6 years ago by 16k • written 9.6 years ago by • 0
2
votes
1
reply
1.3k
views
ChIPpeakAnno: Non-empty IRange object in case of no overlap
chippeakanno iranges
updated 9.4 years ago by ★ 4.3k • written 9.4 years ago by ▴ 30
2
votes
5
replies
1.4k
views
making a RleViewsList object gets slow with many chromosomes
views iranges rle
9.2 years ago Janet Young ▴ 740
2
votes
10
replies
3.5k
views
Extract three types of intergenic regions
granges views annotation iranges
updated 8.5 years ago by ★ 1.7k • written 8.5 years ago by ▴ 50
2
votes
4
replies
4.2k
views
Help with sliding window analysis on GRanges object
IRanges IRanges
10.1 years ago Stefano Iantorno ▴ 30
2
votes
4
replies
1.3k
views
convert a sequence to Ranges object
iranges fasta split
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ★ 1.5k
2
votes
4
replies
1.3k
views
plotting proteases digestion points in a protein
biostrings iranges sequence alignment protein
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ★ 1.5k
2
votes
2
replies
1.4k
views
Number of IRanges elements in TCGA HiSeqV2 dataset
r tcga recount iranges
updated 6.9 years ago by ★ 1.0k • written 6.9 years ago by ▴ 20
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
50 results • Page 1 of 1
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Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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