Showing : GenomicRanges • reset
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
29 days ago gshweta95 • 0
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
9 weeks ago mat149 ▴ 70
2
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1
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250
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Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
11 weeks ago mat149 ▴ 70
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2
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758
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GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 11 months ago by • 0 • written 12 months ago by • 0
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4
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903
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Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 13 months ago by 16k • written 13 months ago by • 0
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575
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Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
15 months ago Delta._.43 ▴ 20
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4
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1.1k
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Flank GenomicRanges on Both Sides
GenomicRanges
updated 15 months ago by 65k • written 15 months ago by ★ 1.5k
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1
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602
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Error printing a CompressedGRangesList
GenomicRanges
15 months ago • updated 14 months ago Lluís Revilla Sancho ▴ 730
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1
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695
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Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 16 months ago by 41k • written 16 months ago by • 0
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2
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1.1k
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GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 17 months ago by ★ 1.6k • written 17 months ago by • 0
2
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2
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1.7k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
19 months ago • updated 18 months ago Mog • 0
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564
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
22 months ago Simon Coetzee ▴ 50
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3
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1.7k
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Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
22 months ago • updated 21 months ago Rodrigo • 0
0
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1
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Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 22 months ago by 65k • written 22 months ago by • 0
3
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2
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1.3k
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toGRanges help!
GenomicRanges toGRanges Bioconductor
23 months ago samantha.haque • 0
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2
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1.5k
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Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.0 years ago vanbelj ▴ 30
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1
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958
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by • 0
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773
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.0 years ago Charles Plessy ▴ 180
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6
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1.5k
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Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 2.1 years ago by 65k • written 2.1 years ago by • 0
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2
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3.6k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.1 years ago by ▴ 20 • written 2.1 years ago by • 0
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672
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Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
2.2 years ago svlachavas ▴ 830
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2
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1.2k
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strand-aware GRanges shift
GenomicRanges
updated 2.2 years ago by ★ 1.6k • written 2.2 years ago by ▴ 10
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9
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3.1k
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Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.3 years ago by 65k • written 2.3 years ago by ▴ 10
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5
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1.8k
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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
4
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1
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733
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`promoters()` fails on `GPos` objects
GenomicRanges
updated 2.4 years ago by 16k • written 2.4 years ago by ▴ 180
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3
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5.1k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 2.5 years ago by 65k • written 2.5 years ago by • 0
2
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4
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2.8k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 2.3 years ago by 16k • written 2.5 years ago by ▴ 20
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2
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1.0k
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Handling missing seqlenghts
GenomicRanges
2.5 years ago Charles Plessy ▴ 180
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2
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1.2k
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GenomicRanges::union fails on R devel
devel GenomicRanges
2.6 years ago Guillaume Devailly ▴ 60
5
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2
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1.1k
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How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
2.6 years ago Pratik Mehta ▴ 10
2
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2
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1.2k
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How to subset GRangesList by seqnames
GenomicRanges
updated 2.6 years ago by 65k • written 2.6 years ago by ▴ 10
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2
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1.3k
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`GenomicRanges` cheat sheet
GenomicRanges
2.6 years ago chirag.parsania • 0
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2
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1.0k
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Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.6 years ago Arslan • 0
0
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2
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935
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GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
2.7 years ago Daniel Cameron ▴ 40
2
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4
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1.2k
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
2.7 years ago • updated 2.6 years ago maltethodberg ▴ 170
0
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1
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616
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How to overlap granges objects by gene name
GenomicRanges
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
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5
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2.5k
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Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
2.8 years ago rtrivedi1 ▴ 10
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0
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662
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Arithmetic Operations Between GRanges' Scores
GenomicRanges
2.9 years ago Dario Strbenac ★ 1.5k
3
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2
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774
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Should I create a new class or using Common Classes
GenomicRanges
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 40
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0
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706
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Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
3.0 years ago alorsonmethyle • 0
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4
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1.4k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
3.0 years ago Yixin • 0
1
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1
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1.1k
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cannot create GRanges object anymore
GenomicR GenomicRanges
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
1
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1
reply
879
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Average coverage between multiple samples
GenomicRanges
updated 3.3 years ago by ★ 11k • written 3.4 years ago by ▴ 90
11
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13
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4.0k
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How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
3.4 years ago • updated 3.2 years ago rohitsatyam102 ▴ 20
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1
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1.2k
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GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
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3
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1.9k
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Merging Neighboring Genomic Segments
Granges GenomicRanges
3.4 years ago rahnaman ▴ 10
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0
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819
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annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
3.5 years ago Nala • 0
0
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0
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1.2k
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Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
3.5 years ago r.a.policastro • 0
2
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2
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1.5k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 3.4 years ago by 16k • written 3.6 years ago by ▴ 80
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1
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1.0k
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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
50 results • Page 1 of 1
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Comment: get BM error by Fara • 0
Thank you for the reply. The examples are these. ENSGACG00000014473 ENSGACG00000015168 ENSGACG00000007529
Comment: get BM error by Mike Smith ★ 6.5k
Can you provide an example of the Ensemble IDs you're trying to convert?
Comment: How to retrieve gene ontology GO class? by bandconductor • 0
Sorry I wasn't clear before. What I mean is the all the information associated with the go term, such as description and evidence. I have …
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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