Showing : GenomicRanges • reset
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Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
updated 5 weeks ago by 43k • written 3.9 years ago by • 0
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Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
updated 5 weeks ago by 43k • written 4.4 years ago by • 0
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
4 months ago info ▴ 10
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ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
5 months ago • updated 12 weeks ago mat149 ▴ 80
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332
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hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
7 months ago user_bioinfo • 0
2
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1
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437
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 10 months ago by 43k • written 10 months ago by ▴ 80
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476
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
11 months ago gshweta95 • 0
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
13 months ago mat149 ▴ 80
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1
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668
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Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
13 months ago mat149 ▴ 80
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2
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1.1k
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GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 22 months ago by • 0 • written 23 months ago by • 0
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1.5k
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Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 2.0 years ago by 16k • written 2.0 years ago by • 0
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948
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Error printing a CompressedGRangesList
GenomicRanges
2.2 years ago • updated 2.1 years ago Lluís Revilla Sancho ▴ 760
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Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.2 years ago Delta._.43 ▴ 20
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2.1k
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Flank GenomicRanges on Both Sides
GenomicRanges
updated 2.2 years ago by 68k • written 2.2 years ago by ★ 1.6k
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1
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Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
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GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 2.3 years ago by ★ 1.6k • written 2.4 years ago by • 0
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2
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2.8k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.5 years ago Mog • 0
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781
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
2.7 years ago Simon Coetzee ▴ 50
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3
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2.7k
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Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
2.7 years ago Rodrigo • 0
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1.4k
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Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
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2
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1.9k
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toGRanges help!
GenomicRanges toGRanges Bioconductor
2.8 years ago samantha.haque • 0
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2
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2.1k
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Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.9 years ago vanbelj ▴ 30
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1.4k
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.9 years ago Charles Plessy ▴ 180
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5.2k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.0 years ago by ▴ 20 • written 3.0 years ago by • 0
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6
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2.0k
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Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
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1.0k
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Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
3.1 years ago svlachavas ▴ 840
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1.6k
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strand-aware GRanges shift
GenomicRanges
updated 3.1 years ago by ★ 1.6k • written 3.1 years ago by ▴ 10
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9
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Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.2 years ago by 68k • written 3.2 years ago by ▴ 10
3
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5
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2.5k
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Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 3.3 years ago by 16k • written 3.3 years ago by ▴ 40
4
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1
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989
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`promoters()` fails on `GPos` objects
GenomicRanges
updated 3.3 years ago by 16k • written 3.3 years ago by ▴ 180
1
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3
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7.2k
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Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 3.4 years ago by 68k • written 3.4 years ago by ▴ 10
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4
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How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 3.2 years ago by 16k • written 3.4 years ago by ▴ 20
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2
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1.5k
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Handling missing seqlenghts
GenomicRanges
3.4 years ago Charles Plessy ▴ 180
4
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2
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1.5k
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GenomicRanges::union fails on R devel
devel GenomicRanges
3.5 years ago Guillaume Devailly ▴ 60
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2
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1.4k
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How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
3.5 years ago Pratik Mehta ▴ 10
2
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2
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1.6k
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How to subset GRangesList by seqnames
GenomicRanges
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 10
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2
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1.8k
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`GenomicRanges` cheat sheet
GenomicRanges
3.5 years ago chirag.parsania ▴ 10
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2
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1.4k
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Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
3.5 years ago Arslan • 0
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2
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1.2k
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GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
3.6 years ago Daniel Cameron ▴ 40
2
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4
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1.6k
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Unique GPos taking into account mcols
GenomicRanges unique GPos
3.6 years ago • updated 3.5 years ago maltethodberg ▴ 180
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856
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How to overlap granges objects by gene name
GenomicRanges
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
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5
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4.0k
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Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
3.7 years ago rtrivedi1 ▴ 10
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Arithmetic Operations Between GRanges' Scores
GenomicRanges
3.8 years ago Dario Strbenac ★ 1.6k
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2
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1.1k
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Should I create a new class or using Common Classes
GenomicRanges
updated 3.8 years ago by 16k • written 3.8 years ago by ▴ 40
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4
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1.9k
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IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
3.9 years ago • updated 3.8 years ago Yixin • 0
11
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13
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5.5k
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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
4.3 years ago • updated 4.1 years ago rohitsatyam102 ▴ 20
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1.4k
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cannot create GRanges object anymore
GenomicR GenomicRanges
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
1
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1
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1.2k
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Average coverage between multiple samples
GenomicRanges
updated 4.2 years ago by ★ 11k • written 4.2 years ago by ▴ 90
20
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10
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21k
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How do I merge a list of GRanges?
GenomicRanges
updated 3.1 years ago by ▴ 40 • written 8.7 years ago by ▴ 40
50 results • Page 1 of 1
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Answer: Use of org.Rn.eg.db with GRCr8 reference genome by James W. MacDonald 68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column by Erika • 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping by James W. MacDonald 68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question? by DavideSant • 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data by silickas • 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
Votes
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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