Showing : granges • reset
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getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
7.2 years ago jerrywu1987 • 0
5
votes
9
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12k
views
subsetByOverlaps : comparing GRANGES and keeping all the information in the METACOLUMNS
granges bedtools intersect
updated 7.2 years ago by ▴ 70 • written 7.2 years ago by ▴ 670
1
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1
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1.4k
views
Subsetting GRanges objext
GRanges subsetting
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
0
votes
7
replies
3.0k
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 7.3 years ago by • 0 • written 7.3 years ago by • 0
2
votes
1
reply
1.7k
views
Error to rename seqlevels in Granges interactions
interactionset granges
updated 7.3 years ago by ★ 29k • written 7.3 years ago by ▴ 40
0
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4
replies
2.3k
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
0
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1
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1.3k
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Detect Sites with Minimum Gap in GRanges Object
R genomicranges granges grange
7.6 years ago g.k • 0
0
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0
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1.3k
views
Metadata sheet for DEXSeq analysis
dexseq differential isoform usage isoforms summarizeoverlaps granges
7.6 years ago A ▴ 60
1
vote
2
replies
2.3k
views
Detecting Overlaps within Grange Object
r grange granges iranges
updated 7.6 years ago by ★ 11k • written 7.6 years ago by • 0
0
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1
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1.2k
views
R_Granges_adding merged Metadata columns
granges findoverlaps
7.6 years ago me.saichi • 0
2
votes
2
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1.2k
views
Features within 2kb window, but with resampling
genomicranges granges slidingwindow
updated 7.6 years ago by ★ 11k • written 7.6 years ago by • 0
2
votes
7
replies
2.4k
views
Splitting lines of a GRanges object based on character list
granges grangeslist
updated 7.6 years ago by ★ 11k • written 7.6 years ago by ▴ 10
3
votes
2
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2.5k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 7.7 years ago by 16k • written 7.7 years ago by ▴ 10
0
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0
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1.3k
views
coercion to Granges from empty data.frame ==> unexpected behavior ??
granges coercion
7.7 years ago Malcolm Cook ★ 1.6k
0
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1
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1.5k
views
Inconsistent Warning: GRanges out of bounds
cn.mops granges trim Genomicranges-method
7.7 years ago znl207 • 0
0
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2
replies
1.4k
views
issue retrieving metadata after psetdiff function
grangeslist granges
7.8 years ago andreag1987 • 0
1
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3
replies
1.8k
views
how to get intron with ensembldb. package?
granges ensembldb GenomicFeatures
7.8 years ago alessandro.pastore ▴ 20
2
votes
3
replies
1.9k
views
GRanges object from gene list
granges bed genomicranges genomeintervals deseq2
7.8 years ago rbronste ▴ 60
2
votes
4
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2.1k
views
Make window around TSS and get values from another data.frame for bins of the specified window
R granges genomicranges chipseq
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ▴ 20
0
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6
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2.7k
views
Add columns to granges object that sum score around range
R Grang r granges rtracklayer
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ▴ 20
2
votes
2
replies
1.7k
views
Packages employing RangedSummarizedExperiment objects
rangedsummarizedexperiment packages granges iranges
updated 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 60
0
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6
replies
4.7k
views
GRanges::distanceToNearest does not return distance to nearest
granges genomicranges
updated 7.9 years ago by ★ 6.8k • written 7.9 years ago by ▴ 40
2
votes
5
replies
1.7k
views
DistanceToNearest Not giving nearest Range
GRanges distancetonearest
updated 7.9 years ago by ★ 4.3k • written 7.9 years ago by ▴ 10
0
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1
reply
1.4k
views
Rcpp adding circular ranges to GRanges object in c++
GRanges circular rcpp IRanges
7.9 years ago hauken_heyken ▴ 80
3
votes
2
replies
1.6k
views
Error when generate mapToGenome
minfi GRanges
updated 7.9 years ago by ▴ 760 • written 7.9 years ago by • 0
0
votes
5
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5.4k
views
Unable to find an inherited method for function distanceToNearest for signature GRanges
chipenrich granges distancetonearest function dataframe
8.0 years ago rbronste ▴ 60
6
votes
4
replies
2.6k
views
unlist a exons GRangeslist object and add a gene name column
granges grangeslist txdb.hsapiens.ucsc.hg19.knowngene
updated 8.0 years ago by 16k • written 8.0 years ago by ▴ 200
0
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1
reply
1.5k
views
predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
8.0 years ago tony j • 0
2
votes
5
replies
1.8k
views
Weaknesses with GRanges data type, or just me ?
GRangeslist GRanges makeGrangesFromDataFrame
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ▴ 80
4
votes
17
replies
4.3k
views
How to construct a valid GRanges object from RCPP and pass back to R
GRanges IRanges RCPP Constructor
updated 8.0 years ago by ▴ 10 • written 8.1 years ago by ▴ 80
1
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1
reply
1.5k
views
Finding distance between end of all ORFs in utr and start of first cds exon in transcript coordinates
granges distance
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ▴ 80
6
votes
2
replies
1.2k
views
Combine 5' leaders and 1st exon of cds into GRangesList
GRanges mapToTranscripts
8.0 years ago hauken_heyken ▴ 80
2
votes
3
replies
2.6k
views
subsetByOverlaps with Multimapping
genomicranges subsetbyoverlaps granges findoverlaps
8.1 years ago Assa Yeroslaviz ★ 1.5k
3
votes
2
replies
2.4k
views
about setdiff() and meta-information in GRanges
granges genomicranges
updated 8.1 years ago by 16k • written 8.1 years ago by ▴ 670
0
votes
4
replies
3.4k
views
an error on GRanges
granges
8.1 years ago Bogdan ▴ 670
1
vote
4
replies
2.0k
views
IRanges (GRanges): Inconsistent behaviour when overlapping ranges of width 0
Iranges granges
updated 8.1 years ago by 16k • written 8.2 years ago by ▴ 40
4
votes
3
replies
5.0k
views
subsetting GRanges object based on gene IDs
genomicranges genomicfeatures granges subsetting
8.1 years ago Assa Yeroslaviz ★ 1.5k
0
votes
3
replies
4.5k
views
makeTxDbFromGFF Error: subscript contains NAs
genomicfeatures granges maketxdbfromgff
updated 8.2 years ago by 16k • written 8.3 years ago by • 0
0
votes
3
replies
2.0k
views
Using IRanges to find gene TSS that overlap a window
iranges R granges
updated 8.2 years ago by • 0 • written 8.2 years ago by ▴ 20
2
votes
3
replies
1.7k
views
How to find nearest CpG islands around miRNA genes using granges?
granges bioconductor R
8.2 years ago Adam_M • 0
0
votes
3
replies
2.5k
views
IRanges from BAM file to GRanges convert
iranges granges
8.2 years ago seungjoon.kim • 0
0
votes
8
replies
3.2k
views
Isoforms detection using bioconductor
bioconductor biomart granges rna-seq
updated 8.2 years ago by ★ 11k • written 8.2 years ago by • 0
3
votes
15
replies
4.1k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 8.2 years ago by ★ 11k • written 8.2 years ago by ★ 1.5k
0
votes
1
reply
1.4k
views
reduce granges if mcols value are ideitical with the next intervals
granges reduce
8.3 years ago alessandro.pastore ▴ 20
3
votes
2
replies
1.8k
views
matrix as a column of mcols of GRanges would not be extracted correctly by lapply
mcols DataFrame GRanges
updated 8.3 years ago by ★ 11k • written 8.3 years ago by ▴ 30
1
vote
1
reply
1.3k
views
Width in IRanges objects on "+" and "-" strand
iranges granges grangeslist
updated 8.3 years ago by ★ 11k • written 8.3 years ago by ▴ 10
1
vote
6
replies
13k
views
How to change seqlevels in a GRanges object
GRanges
updated 8.3 years ago by ★ 1.3k • written 8.3 years ago by ▴ 110
0
votes
2
replies
1.7k
views
sortSeqlevels is not sorting for GRanges object
GRanges
updated 8.3 years ago by ★ 11k • written 8.3 years ago by ▴ 110
5
votes
9
replies
2.5k
views
reduce function after combining 2 GRanges objects from cn.mops output
GRanges cn.mops
updated 8.3 years ago by ★ 11k • written 8.3 years ago by ▴ 110
3
votes
1
reply
5.9k
views
Creating a count matrix from 8 bam files in R (RNAseq experiment)
deseq2 rnaseq count matrix galignments granges
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 10
206 results • Page 2 of 5
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Comment: Using DESeq2 for age prediction by ATpoint ★ 5.0k
You sure will find online tutorials on regression models / machine learning classifiers. The support site is for help with Bioconductor. Ch…
Comment: Using DESeq2 for age prediction by picasa1983 • 0
Thanks ! Do you have any idea how to do that ?
Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
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