Showing : genomicranges • reset
2
votes
1
reply
141
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 11 days ago by 42k • written 11 days ago by ▴ 70
0
votes
0
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140
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
7 weeks ago gshweta95 • 0
0
votes
0
replies
211
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
3 months ago mat149 ▴ 70
2
votes
1
reply
292
views
Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
3 months ago mat149 ▴ 70
4
votes
5
replies
3.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 3 months ago by ▴ 10 • written 8.5 years ago by ▴ 10
0
votes
2
replies
787
views
GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 12 months ago by • 0 • written 12 months ago by • 0
5
votes
6
replies
9.4k
views
Merge multiple genomic intervals if overlapping more than xx percents
genomicranges
written 9.0 years ago by ▴ 140
3
votes
4
replies
962
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 14 months ago by 16k • written 14 months ago by • 0
0
votes
1
reply
640
views
Error printing a CompressedGRangesList
GenomicRanges
16 months ago • updated 14 months ago Lluís Revilla Sancho ▴ 730
0
votes
0
replies
611
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
16 months ago Delta._.43 ▴ 20
4
votes
4
replies
1.2k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 16 months ago by 65k • written 16 months ago by ★ 1.5k
3
votes
1
reply
722
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 17 months ago by 42k • written 17 months ago by • 0
0
votes
2
replies
1.2k
views
GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 18 months ago by ★ 1.6k • written 18 months ago by • 0
2
votes
2
replies
1.8k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
19 months ago Mog • 0
8
votes
12
replies
5.5k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 22 months ago by • 0 • written 9.2 years ago by ▴ 20
2
votes
3
replies
1.8k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
22 months ago Rodrigo • 0
0
votes
0
replies
585
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
22 months ago Simon Coetzee ▴ 50
0
votes
1
reply
982
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 22 months ago by 65k • written 22 months ago by • 0
3
votes
2
replies
1.3k
views
toGRanges help!
GenomicRanges toGRanges Bioconductor
2.0 years ago samantha.haque • 0
1
vote
2
replies
1.5k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.1 years ago vanbelj ▴ 30
0
votes
1
reply
987
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
1
vote
0
replies
791
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.1 years ago Charles Plessy ▴ 180
0
votes
2
replies
3.7k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.1 years ago by ▴ 20 • written 2.2 years ago by • 0
15
votes
4
replies
11k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 2.1 years ago by 16k • written 7.9 years ago by ▴ 40
0
votes
6
replies
1.5k
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 2.2 years ago by 65k • written 2.2 years ago by • 0
5
votes
8
replies
8.8k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 2.3 years ago by • 0 • written 8.6 years ago by ▴ 50
0
votes
0
replies
713
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
2.3 years ago svlachavas ▴ 830
6
votes
2
replies
1.2k
views
strand-aware GRanges shift
GenomicRanges
updated 2.3 years ago by ★ 1.6k • written 2.3 years ago by ▴ 10
19
votes
10
replies
18k
views
How do I merge a list of GRanges?
GenomicRanges
updated 2.3 years ago by ▴ 40 • written 7.9 years ago by ▴ 40
2
votes
4
replies
2.9k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 2.3 years ago by 16k • written 2.6 years ago by ▴ 20
9
votes
9
replies
3.2k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.4 years ago by 65k • written 2.4 years ago by ▴ 10
3
votes
5
replies
1.9k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 2.4 years ago by 16k • written 2.4 years ago by ▴ 40
0
votes
1
reply
1.4k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 2.5 years ago by • 0 • written 8.5 years ago by ▴ 10
4
votes
1
reply
765
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 2.5 years ago by 16k • written 2.5 years ago by ▴ 180
0
votes
3
replies
5.2k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 2.5 years ago by 65k • written 2.5 years ago by • 0
0
votes
2
replies
1.1k
views
Handling missing seqlenghts
GenomicRanges
2.6 years ago Charles Plessy ▴ 180
4
votes
2
replies
1.2k
views
GenomicRanges::union fails on R devel
devel GenomicRanges
2.6 years ago Guillaume Devailly ▴ 60
2
votes
4
replies
1.2k
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
2.8 years ago • updated 2.6 years ago maltethodberg ▴ 180
5
votes
2
replies
1.1k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
2.7 years ago Pratik Mehta ▴ 10
2
votes
2
replies
1.2k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 2.7 years ago by 65k • written 2.7 years ago by ▴ 10
2
votes
2
replies
1.4k
views
`GenomicRanges` cheat sheet
GenomicRanges
2.7 years ago chirag.parsania • 0
0
votes
2
replies
1.1k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.7 years ago Arslan • 0
0
votes
2
replies
961
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
2.8 years ago Daniel Cameron ▴ 40
0
votes
1
reply
631
views
How to overlap granges objects by gene name
GenomicRanges
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
votes
5
replies
2.7k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
2.9 years ago rtrivedi1 ▴ 10
7
votes
5
replies
1.9k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 6.0 years ago by ▴ 140
0
votes
0
replies
677
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
2.9 years ago Dario Strbenac ★ 1.5k
3
votes
2
replies
810
views
Should I create a new class or using Common Classes
GenomicRanges
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 40
0
votes
1
reply
1.1k
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 3.0 years ago by • 0 • written 5.0 years ago by • 0
1
vote
4
replies
1.5k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
3.1 years ago • updated 3.0 years ago Yixin • 0
50 results • Page 1 of 1
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Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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