Showing : Genomicranges • reset
4
votes
4
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5.2k
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How to bin a GRanges to small bins
GenomicRanges
updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 200
9
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21
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13k
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annotate GRanges with upstream or downstream nearest gene
GRange genomicranges genomicfeatures
updated 9.7 years ago by ★ 1.3k • written 9.7 years ago by ▴ 200
1
vote
4
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1.7k
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subsetting a GRanges object with IntegerList and CharacterList metadata columns
granges genomicranges
updated 9.8 years ago by ★ 11k • written 9.8 years ago by ▴ 10
1
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2
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1.3k
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How to find similar ranges without algorithm="intervaltree"
granges genomicranges iranges
updated 9.8 years ago by 16k • written 9.8 years ago by ▴ 40
2
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2
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1.5k
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Efficiently finding a relative position inside a GRanges object
genomicranges
9.8 years ago Aliaksei Holik ▴ 350
2
votes
10
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2.9k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 9.8 years ago by ★ 11k • written 9.8 years ago by ▴ 10
0
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1
reply
1.7k
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How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 3.8 years ago by • 0 • written 9.8 years ago by ▴ 10
4
votes
5
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4.0k
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How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 20 months ago by ▴ 10 • written 9.8 years ago by ▴ 10
1
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11
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3.0k
views
Had to remove duplicated() in order to install GenomicRanges 1.22 on top of 1.20 on linux
installation genomicranges summarizedexperiment
9.9 years ago • updated 9.8 years ago knb • 0
1
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3
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2.2k
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issue renaming seqnames in genomic ranges
genomicranges
updated 9.8 years ago by ★ 11k • written 9.8 years ago by ▴ 90
1
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1
reply
1.0k
views
Concatenate individual genomic intervals into populational regions
genomicranges
updated 9.8 years ago by 16k • written 9.8 years ago by ▴ 40
1
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6
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2.8k
views
Error: subsetting GenomicRanges with disjoint ranges produces errors
software error genomicranges
9.8 years ago ripkrizbi • 0
3
votes
2
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2.1k
views
how much positions overlapped for each pair of the pairs obtained by findoverlap.
granges genomicranges findoverlaps subsetbyoverlaps
updated 9.9 years ago by 16k • written 9.9 years ago by ▴ 50
1
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10
replies
3.2k
views
GenomicRanges bug in follow?
genomicranges
10.0 years ago • updated 9.9 years ago Janet Young ▴ 740
0
votes
6
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5.4k
views
Package ‘GenomicRanges’ version 1.20.8 cannot be unloaded
rapidr genomicranges
9.9 years ago Pau Marc Muñoz Torres ▴ 20
3
votes
6
replies
3.1k
views
Assign genes to CpG islands
annotation genomicranges bsgenome
updated 9.9 years ago by ★ 1.3k • written 9.9 years ago by ▴ 10
4
votes
6
replies
2.1k
views
GenomicRanges mapply to all combinations of GRangesList objects
genomicranges mapply grangeslist
9.9 years ago francesca casalino ▴ 50
0
votes
2
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967
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Package GenomicRanges missing functions and classes related to Gapped Alignments
genomicranges
10.0 years ago jduffner • 0
4
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2
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1.8k
views
How to find particular types of overlap with GenomicRanges
r genomicranges iranges
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 50
17
votes
4
replies
13k
views
How to use GenomicRanges to find overlaps by percentage covered of interval
genomicranges
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 50
2
votes
5
replies
4.9k
views
GRanges - add names when constructing a new GRanges, rather than afterwards?
genomicranges
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 740
2
votes
2
replies
1.5k
views
Can precede() and follow() in some cases return identical output?
genomicranges
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Feature Request: improve output when printing GenomicRanges instances
GenomicRanges featurerequest
10.0 years ago Keith Hughitt ▴ 180
3
votes
7
replies
2.6k
views
Intersecting a Granges and a GRangesList elementwise
findoverlaps genomicranges
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 150
1
vote
1
reply
2.0k
views
Using findOverlaps to find only partial overlaps
findoverlaps genomicranges
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 150
2
votes
12
replies
2.3k
views
remove set number of nucleotides from each gene's cds region in GRangesList
genomicranges genomicfeatures
updated 10.0 years ago by ★ 11k • written 10.1 years ago by ▴ 90
0
votes
2
replies
2.3k
views
Problem with Finding Mean Coverage using binnedAverage function
GenomicRanges
updated 10.1 years ago by 16k • written 10.1 years ago by • 0
5
votes
10
replies
4.0k
views
tileGenome for overlapping ranges?
genomicranges
updated 10.1 years ago by • 0 • written 10.6 years ago by ▴ 740
0
votes
3
replies
1.8k
views
narrow function for GRangesList objects?
genomicranges
10.1 years ago Janet Young ▴ 740
1
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3
replies
2.7k
views
summarizeOverlaps bplapply error
genomicalignments genomicranges bioconductor rnaseq
updated 10.1 years ago by • 0 • written 10.6 years ago by • 0
8
votes
9
replies
6.7k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 10.2 years ago by • 0 • written 10.2 years ago by ★ 1.5k
0
votes
6
replies
3.9k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster quasR genomicfeatures genomicranges alignment
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 70
1
vote
2
replies
2.3k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 90
11
votes
0
replies
6.4k
views
Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
10.2 years ago Martin Morgan 25k
2
votes
7
replies
5.0k
views
coverage over specific GenomicRanges
genomicranges
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 90
1
vote
1
reply
3.8k
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bedtools like subtract in genomic ranges?
genomicranges
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 90
0
votes
1
reply
1.9k
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Newbie - Adding Labels to Individual Genes with ggbio?
r ggbio ggplot2 dnaseq genomicranges
updated 10.2 years ago by ▴ 130 • written 10.2 years ago by • 0
1
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2
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1.1k
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GRanges / IRanges maxgap behaviour change raises no warning
genomicranges granges iranges
updated 10.3 years ago by 16k • written 10.3 years ago by ▴ 40
5
votes
6
replies
11k
views
Merge multiple genomic intervals if overlapping more than xx percents
genomicranges
written 10.3 years ago by ▴ 140
3
votes
2
replies
2.1k
views
Subset SummarizedExperiment/GRangesList by seqnames
genomicranges
updated 10.4 years ago by ▴ 70 • written 10.4 years ago by 43k
17
votes
4
replies
18k
views
How to properly sort GRanges?
granges genomicranges sort seqnames order
updated 10.4 years ago by ▴ 30 • written 10.8 years ago by ▴ 680
0
votes
2
replies
2.1k
views
Calculate the expression of gene
genomicranges iranges
updated 10.5 years ago by 68k • written 10.5 years ago by ▴ 20
0
votes
7
replies
2.2k
views
Speeding up or replacing Loops to process Bam Reads
genomicranges reads genomicfeatures Bam
10.5 years ago gen ▴ 30
0
votes
3
replies
2.8k
views
problem with cbind on GRanges object - new bug?
genomicranges cbind
10.5 years ago Janet Young ▴ 740
2
votes
1
reply
2.6k
views
Change the start of GenomicRanges list
genomicranges
updated 10.5 years ago by 16k • written 10.5 years ago by ▴ 90
1
vote
1
reply
1.5k
views
removing reads from coverage() calculation.
bam rsamtools genomicranges
updated 10.6 years ago by 25k • written 10.6 years ago by ▴ 30
5
votes
8
replies
3.8k
views
Large disk images of DESeqDataSet / SummarizedExperiment objects when using the save function
SummarizedExperiment DESeqDataSet GenomicRanges DESeq2 save
updated 10.6 years ago by ★ 13k • written 10.6 years ago by ▴ 30
4
votes
1
reply
7.7k
views
how to get genomic coordinates for a list of genes
genomicranges
updated 10.6 years ago by 21k • written 10.6 years ago by ▴ 50
4
votes
2
replies
3.6k
views
extracting distance from Hits object
genomicranges iranges
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 140
3
votes
5
replies
3.8k
views
Element-wise setdiff when psetdiff fails for GenomicRanges
genomicranges iranges genomics
updated 10.7 years ago by ▴ 60 • written 10.7 years ago by ▴ 150
403 results • Page 6 of 9
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Answer: readBam vs read_bam_insert_metrics by lincolnprice964 • 0
Yes read_bam_insert_metrics() can take input directly from a BAM file or from an object created with readBam(). Use whichever fits best in …
Comment: DESeq2 interactions by lincolnprice964 • 0
If you want HP vs CNP directly, set up the interaction model: dds <- DESeqDataSetFromTximport(genes.salmon, coldata, ~ pollution + temp + …
Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
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Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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