Showing : cn.mops • reset
1
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2
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723
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" 'end' must be >= 'start' - 1" error in cn.mops
cn.mops
20 months ago User000 • 0
0
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3
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1.3k
views
cn.mops segmentation error
cn.mops
updated 21 months ago by • 0 • written 22 months ago by ▴ 40
0
votes
1
reply
566
views
Suspected bug on GetReadCountsFromBAM in cn.mops
cn.mops
3.8 years ago asafpr • 0
0
votes
1
reply
739
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How to use panelcn.mops to detect CNVs from whole genome data by getting count windows from BED file?
cn.mops panelcn.mops CNV detection CNV
4.2 years ago metzgerlukas • 0
0
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0
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477
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cn.mops : undef chromsome using data matrix as input
CNV cn.mops undef
4.2 years ago ankita.narang86 • 0
0
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0
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759
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cn.MOPS output - mean/median of what?
cn.MOPS CNV copy number
4.3 years ago liorglic ▴ 10
0
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1
reply
789
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CNV plot using cn.mops
cnv R plot visualization cn.mops software error
4.5 years ago ari • 0
0
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0
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632
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ChrM causes "missing value where TRUE/FALSE needed" error
cn.mops
4.5 years ago millerh1 ▴ 10
0
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1
reply
869
views
Error using singlecn.mops for cnv detection in WGS data
cnv cn.mops singlecn.mops
updated 2.2 years ago by • 0 • written 4.6 years ago by • 0
0
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2
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1.1k
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problem about using cn.mops
cn.mops
updated 3.0 years ago by • 0 • written 4.9 years ago by • 0
0
votes
3
replies
984
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Error in if (all(x <= minReadCount) & lambda <= minReadCount) { : missing value where TRUE/FALSE needed
cnmops cn.mops error
updated 5.0 years ago by 25k • written 5.0 years ago by • 0
1
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4
replies
951
views
cn.mops on CRAM files
cn.mops
updated 5.0 years ago by ▴ 540 • written 5.0 years ago by • 0
2
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3
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1.3k
views
mosdepth output into cn.mops?
cn.mops
updated 5.2 years ago by ▴ 540 • written 5.2 years ago by • 0
0
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0
replies
673
views
cn.mops normalization of multiple samples
cn.mops
5.3 years ago DannyM • 0
0
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0
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974
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Mean and median values in cn.mops cnvs output
cn.mops referencecn.mops
updated 5.4 years ago by 0 • written 5.5 years ago by • 0
0
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3
replies
958
views
tumor vs control: multiple samples
cn.mops
5.4 years ago DannyM • 0
0
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1
reply
981
views
cn.MOPS: Error in getReadCountsFromBAM
cn.mops
5.7 years ago laurabuggiotti • 0
0
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0
replies
976
views
Doubt about the interpretation of cn.mops tumor vs normal results
cn.mops dnaseq bioinformatics
5.8 years ago Cased • 0
0
votes
0
replies
682
views
How to interpret out of referencecn.mops
referencecn.mops cn.mops
5.8 years ago eddie.kaho.ho • 0
0
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18
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4.5k
views
cn.MOPs: Error in value[[3L]](cond) :
cn.mops
updated 5.9 years ago by ▴ 540 • written 5.9 years ago by • 0
2
votes
3
replies
1.5k
views
Doubt about WL in cn.mops
dnacopy dnaseq genomic cn.mops cnv
updated 5.9 years ago by ▴ 540 • written 5.9 years ago by • 0
0
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1
reply
888
views
cn.mops: interpreting output when returnPosterior=TRUE
cn.mops
updated 6.1 years ago by ▴ 540 • written 6.1 years ago by • 0
0
votes
2
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1.0k
views
best way to normalize for differences in sample read depth: normalize genome vs cn.MOPs
cn.mops normalization
updated 14 months ago by • 0 • written 6.2 years ago by • 0
1
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2
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1.8k
views
cn.MOPS error: Error in if (WL >= sl[i]) { : missing value where TRUE/FALSE needed
cn.mops
6.3 years ago hugo.magalhaes ▴ 10
0
votes
1
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1.0k
views
Inconsistent Warning: GRanges out of bounds
cn.mops granges trim Genomicranges-method
6.3 years ago znl207 • 0
0
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1
reply
978
views
Error with plotting with target sequencing data
cn.mops
updated 6.3 years ago by ▴ 540 • written 6.3 years ago by • 0
2
votes
6
replies
2.6k
views
Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error cn.mops
updated 12 weeks ago by • 0 • written 6.4 years ago by ▴ 10
0
votes
5
replies
1.5k
views
Error when use getSegmentReadCountsFromBAM
targeted sequencing cn.mops
6.4 years ago jinxinhao1988 • 0
0
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2
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1.5k
views
cn.MOPs issue with "Error in if (all(segMedianT == 0))"
cn.mops cnv
updated 6.5 years ago by ▴ 540 • written 6.5 years ago by ▴ 20
0
votes
4
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1.3k
views
Is cn.mops can be used for detecting CNV for targeted sequencing of 8M region
cn.mops
updated 6.5 years ago by ▴ 540 • written 6.5 years ago by • 0
5
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7
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1.5k
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about the runs with cn.mops
cn.mops referencecn.mops
6.8 years ago • updated 6.7 years ago Bogdan ▴ 670
1
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2
replies
1.6k
views
cn.MOPS - reporting log normalized read counts as table
cn.mops log normalized counts table
updated 6.9 years ago by ▴ 540 • written 6.9 years ago by • 0
0
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1
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1.1k
views
getReadCountsFromBAM including bed information
cn.mops bed files getReadCountsFromBAM
6.9 years ago Pau Marc Muñoz Torres ▴ 20
5
votes
9
replies
1.9k
views
reduce function after combining 2 GRanges objects from cn.mops output
GRanges cn.mops
updated 6.9 years ago by ★ 11k • written 6.9 years ago by ▴ 110
2
votes
1
reply
1.0k
views
How to combine CNVDetectionResult objects in cn.mops package
cn.mops
updated 6.9 years ago by ▴ 540 • written 6.9 years ago by ▴ 110
0
votes
2
replies
1.2k
views
getReadCountsFromBAM and paired-end reads
cn.mops
7.0 years ago Alexandre Kuhn ▴ 20
4
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2
replies
1.5k
views
using cn.MOPS on WES data GERMLINE-TUMOR
cn.mops
7.0 years ago Bogdan ▴ 670
0
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2
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1.3k
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Conflict in cnvr and cnvs result from cn.mops
cn.mops
updated 7.0 years ago by ▴ 540 • written 7.1 years ago by • 0
0
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4
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1.3k
views
cn.mops encounter negative width problem
cn.mops referencecn.mops
updated 7.1 years ago by ▴ 540 • written 7.1 years ago by • 0
3
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1
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1.2k
views
R code for cn.mops -- if a chromosome does not have CNV ?
cn.mops referencecn.mops
updated 7.1 years ago by ▴ 540 • written 7.3 years ago by ▴ 670
3
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5
replies
1.6k
views
R code for cn.mops
cn.mops
updated 14 months ago by • 0 • written 7.3 years ago by ▴ 670
1
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1
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983
views
which cn.mops function should I use
cn.mops
updated 7.1 years ago by ▴ 540 • written 7.1 years ago by • 0
0
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1
reply
1.1k
views
cn.mops returning only "NA" as copy number
cn.mops
updated 7.2 years ago by ▴ 540 • written 7.2 years ago by • 0
0
votes
2
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1.4k
views
about an error in cn.MOPS : could not find symbol "recursive" in environment of the generic function
cn.MOPS
7.3 years ago Bogdan ▴ 670
4
votes
3
replies
1.3k
views
parameter "refSeqName" in function "getReadCountsFromBAM"
cn.mops
updated 7.3 years ago by ▴ 540 • written 7.8 years ago by • 0
0
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4
replies
1.4k
views
Call CNV in population with large depth variance
cn.mops
updated 7.4 years ago by ▴ 540 • written 7.4 years ago by • 0
4
votes
9
replies
2.4k
views
How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
cn.mops cnv targeted sequencing
updated 7.4 years ago by ▴ 540 • written 7.4 years ago by ▴ 20
0
votes
1
reply
859
views
Input (X) data type is not numeric if read from GRanges obj
cn.mops
updated 7.4 years ago by ▴ 540 • written 7.4 years ago by • 0
1
vote
2
replies
1.2k
views
cn.mops: NA in the output of referencecn.mops
cn.mops referencecn.mops
updated 7.5 years ago by ▴ 540 • written 7.5 years ago by ▴ 90
0
votes
2
replies
1.1k
views
about cn.MOPS: paired vs unpaired
cn.mops
updated 7.6 years ago by ▴ 540 • written 7.6 years ago by ▴ 670
50 results • Page 1 of 1
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Comment: How to compare subset of samples from VCF files by Gordon Smyth 50k
Welcome to Bioconductor support. Did you know that you can delete your old postings if they haven't received an answer yet? Instead of ap…
Comment: How to compare subset of samples from VCF files by Marco • 0
Here's the vcf file as code block ``` ##fileformat=VCFv4.2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth"> ##FOR…
Comment: Gviz and custom database by James W. MacDonald 66k
The vignette for `Gviz` says you can use a `DNAStringSet`, generated using `Biostrings`. Have you tried that?
Comment: Gviz and custom database by luigi.faino • 0
Dear, this is not what I need. I need to transform a fasta sequence in a genome track usable in Gviz. L
Answer: Gviz and custom database by James W. MacDonald 66k
https://bioconductor.org/packages/release/bioc/vignettes/txdbmaker/inst/doc/txdbmaker.html
Votes
Answer: makeExampleDESeqDataSet using pilot data
Answer: Checking/updating package versions
Answer: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
convert data frame of Entrez IDs to Gene Symbols
Answer: LRT, pairwise comparisons and p-value adjustment
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