Showing : Genomicranges • reset
2
votes
3
replies
2.1k
views
GenomicRanges_RaggedExperiment Error in as background, class mcol no method or default for coercing logical to factor
genomicranges RaggedExperiment coercion logical factor
updated 7.8 years ago by 700 • written 7.8 years ago by • 0
2
votes
4
replies
2.3k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 7.9 years ago by 16k • written 7.9 years ago by ▴ 40
3
votes
4
replies
7.2k
views
Subset GRanges object into new object
R genomicranges subsetting
7.9 years ago jhanks1981 • 0
0
votes
0
replies
1.1k
views
resize functions causes an error - "could not find function "unsafe.update"
genomicranges iranges resize
7.9 years ago Assa Yeroslaviz ★ 1.5k
0
votes
0
replies
1.2k
views
Calculate the CNV frequency in a dataset
genomicranges cnvtools
7.9 years ago julrodr80 ▴ 30
0
votes
2
replies
1.0k
views
Error in binning bam files
R makeBinnedCountsFile GenomicRanges
7.9 years ago greeshmathulasi1 • 0
0
votes
1
reply
1.2k
views
GenomicRanges: Possible Bug
genomicranges bug
updated 7.9 years ago by 68k • written 7.9 years ago by • 0
4
votes
2
replies
1.6k
views
Split Genome into 2kb bins GenomicRanges
genomicranges
updated 8.0 years ago by 16k • written 8.0 years ago by ▴ 10
6
votes
6
replies
2.1k
views
Implementing fast mathematical and statistical operations on genomic variables in bioconductor
genomicranges biocgenerics rlelist genomicvars iranges
updated 8.0 years ago by 16k • written 8.0 years ago by ▴ 20
6
votes
6
replies
7.3k
views
converting a GRangesList object with different lengths into a data frame
genomicranges grangeslist dataframe irangeslist lists
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ★ 1.5k
0
votes
4
replies
1.5k
views
Problem with IRanges and GenomicRanges
iranges genomicranges
updated 8.0 years ago by 16k • written 8.0 years ago by • 0
2
votes
2
replies
1.8k
views
Error in normSplitFactor(f, x)
GenomicRanges rtracklayer goseq
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ▴ 10
2
votes
2
replies
1.4k
views
Not getting the expected answers from GenomicRanges follow/precede
GenomicRanges
updated 8.0 years ago by ★ 6.8k • written 8.0 years ago by ▴ 20
0
votes
3
replies
2.3k
views
cannot get GRanges() to load
GenomicRanges
updated 8.0 years ago by ▴ 140 • written 8.0 years ago by • 0
2
votes
3
replies
2.6k
views
subsetByOverlaps with Multimapping
genomicranges subsetbyoverlaps granges findoverlaps
8.0 years ago Assa Yeroslaviz ★ 1.5k
3
votes
2
replies
2.4k
views
about setdiff() and meta-information in GRanges
granges genomicranges
updated 8.0 years ago by 16k • written 8.0 years ago by ▴ 670
4
votes
3
replies
5.0k
views
subsetting GRanges object based on gene IDs
genomicranges genomicfeatures granges subsetting
8.0 years ago Assa Yeroslaviz ★ 1.5k
3
votes
13
replies
3.3k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder genomicfeatures genomicranges
updated 8.1 years ago by ★ 1.1k • written 8.1 years ago by ▴ 20
7
votes
12
replies
3.0k
views
Extract isoform-specific ranges
bioconductor genomicranges
updated 8.1 years ago by ★ 1.6k • written 8.1 years ago by ▴ 10
0
votes
0
replies
2.0k
views
Gviz plot with two GRanges: "The track chromosomes in 'trackList' differ. Setting all tracks to chromosome 'chr14'"
gviz genomicranges
8.1 years ago rtonalli • 0
2
votes
5
replies
2.0k
views
Getting error using GenomicRanges::setdiff
GenomicRanges setdiff
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 110
2
votes
1
reply
2.0k
views
Extracting UTRs from exon and CDS data
genomeintervals UTRs exons CDS GenomicRanges
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 110
1
vote
0
replies
2.9k
views
as.data.table method for GRanges modifies the original object by reference
genomicranges data.table
8.1 years ago alex.gos90 ▴ 10
1
vote
6
replies
4.6k
views
reduce function in GenomicRanges
genomicranges reduce
updated 8.1 years ago by 16k • written 8.2 years ago by ▴ 20
0
votes
2
replies
1.3k
views
How to suppress the out-of-bound warnings in GenomicRanges function resize()
genomicranges resize
updated 8.2 years ago by 16k • written 8.2 years ago by ▴ 20
1
vote
5
replies
2.6k
views
Error creating DESeqDataSet from "airway" SummarizedExperiment
deseq2 genomicranges
updated 8.2 years ago by 16k • written 8.2 years ago by ★ 1.1k
0
votes
10
replies
2.7k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
8.2 years ago lovro0 ▴ 10
0
votes
2
replies
2.7k
views
Exporting a GenomicRanges object as GTF/GFF file
genomicranges rtracklayer gtf gff export
8.2 years ago rubi ▴ 110
3
votes
2
replies
1.4k
views
GenomicRanges::gaps() not working as expected
genomicranges
8.3 years ago jfiksel ▴ 30
0
votes
1
reply
870
views
binnedaverage - is it possible to add an na.rm option?
genomicranges
updated 8.3 years ago by 16k • written 8.3 years ago by ▴ 740
2
votes
3
replies
1.6k
views
Split Genomic Ranges With Reference Overlaps (Centromere)
granges genomicranges split
written 8.3 years ago by • 0
2
votes
2
replies
1.4k
views
Findoverlaps insame sample
genomicranges granges findoverlaps
8.3 years ago julrodr80 ▴ 30
2
votes
1
reply
1.6k
views
GenomicAlignments/access correct bp positions near indels
genomicranges genomicalignments snp
updated 8.3 years ago by 16k • written 8.3 years ago by ▴ 90
0
votes
7
replies
2.8k
views
regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder GenomeInfoDb GenomicRanges
8.4 years ago • updated 8.3 years ago Wayne • 0
0
votes
1
reply
1.2k
views
Genomic Ranges package not working
genomicranges assay
updated 8.4 years ago by 25k • written 8.4 years ago by • 0
2
votes
1
reply
1.2k
views
pintersect and psetdiff changed behavior
genomicranges
updated 8.5 years ago by ★ 11k • written 8.5 years ago by ▴ 90
0
votes
0
replies
1.2k
views
minfi "mapToGenome" : Error in as.vector(x, mode) : '.SigArgs' is shorter than '.SigLength' says it should be
minfi GenomicRanges
8.5 years ago cathy.philippe • 0
0
votes
2
replies
1.4k
views
DESeq2 Error in .Primitive("c")(<S4 object of class "GRangesList">
deseq2 genomicranges differential gene expression
8.5 years ago erin.gill81 ▴ 60
0
votes
5
replies
1.9k
views
TxDb.Hsapiens.UCSC.hg19.knownGene - Error: subscript contains out-of-bounds indices for some Entrez codes
bioconductor genomicranges homo sapiens
updated 8.5 years ago by 68k • written 8.5 years ago by • 0
0
votes
1
reply
1.8k
views
IRanges object from count matrix
genomicranges iranges featurecounts counts rnaseq
updated 8.6 years ago by 16k • written 8.6 years ago by ★ 1.5k
0
votes
3
replies
2.1k
views
findOverlaps() error after updating package
GenomicRanges findOverlaps
updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 20
2
votes
2
replies
1.5k
views
Integer overflow when tabulating read coverage
genomicalignments genomicranges
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ▴ 70
6
votes
4
replies
1.7k
views
Aggregate read counts by non-uniform overlapping sliding windows
granges genomicranges featurecounts
updated 8.7 years ago by ★ 11k • written 8.7 years ago by ▴ 20
0
votes
2
replies
1.4k
views
Why does a `first_time` object appear when showing GRangesList object?
genomicranges grangeslist
updated 8.7 years ago by 68k • written 8.7 years ago by • 0
2
votes
2
replies
1.5k
views
update the version of GenomicRanges
genomicranges
updated 8.7 years ago by ▴ 10 • written 8.7 years ago by • 0
3
votes
21
replies
3.9k
views
`precede` does not perform as expected
genomicranges precede ph525.5x
8.7 years ago wcstcyx ▴ 30
2
votes
4
replies
2.1k
views
Calculate fraction of bases (GRanges) that have non-zero coverage (RleList)
genomicalignments genomicranges
8.7 years ago jma1991 ▴ 70
0
votes
4
replies
1.7k
views
How to find the distance between the integration site and gene
hiAnnotator genomicranges
updated 8.7 years ago by ★ 11k • written 8.7 years ago by • 0
0
votes
2
replies
1.6k
views
problem with makeGRangesListFromFeatureFragments
genomicranges iranges irangeslist grangeslist
updated 8.7 years ago by 4.2k • written 8.8 years ago by • 0
1
vote
5
replies
1.8k
views
Obtain the specific range that overlap
overlap genomicranges range
8.8 years ago julrodr80 ▴ 30
403 results • Page 4 of 9
Recent ...
Replies
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Comment: Average biological replicates in RNA-seq by boczniak767 ▴ 740
@atpoint Should I first standardise data and then average replicates?
Comment: 3-factor DESeq2 trime-series analysis by gogeni5529 • 0
Thans you @swbarnes2 for the answer. I can see why trying to include all three parameters might be difficult to interpret. But we're inte…
Comment: 3-factor DESeq2 trime-series analysis by swbarnes2 ★ 1.4k
What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by yongjie.wang • 0
Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…
Votes
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?
Awards • All
Popular Question to Assa Yeroslaviz ★ 1.5k
Popular Question to Nik dAK ▴ 10
Popular Question to Michael • 0
Popular Question to sum31278 • 0
Popular Question to Gordon Smyth 53k
Locations • All
United States, 17 minutes ago
Spain, 25 minutes ago
Poland, 56 minutes ago
United States, 1 hour ago
Pittsburgh, United States, 1 hour ago
Traffic: 858 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6