Showing : cn.MOPS • reset
1
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2
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698
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" 'end' must be >= 'start' - 1" error in cn.mops
cn.mops
19 months ago User000 • 0
0
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3
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1.2k
views
cn.mops segmentation error
cn.mops
updated 20 months ago by • 0 • written 21 months ago by ▴ 40
0
votes
1
reply
555
views
Suspected bug on GetReadCountsFromBAM in cn.mops
cn.mops
3.7 years ago asafpr • 0
0
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0
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462
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cn.mops : undef chromsome using data matrix as input
CNV cn.mops undef
4.1 years ago ankita.narang86 • 0
0
votes
1
reply
718
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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
4.1 years ago metzgerlukas • 0
0
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0
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743
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cn.MOPS output - mean/median of what?
cn.MOPS CNV copy number
4.2 years ago liorglic ▴ 10
0
votes
1
reply
762
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CNV plot using cn.mops
cnv R plot visualization cn.mops software error
4.4 years ago ari • 0
0
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0
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610
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ChrM causes "missing value where TRUE/FALSE needed" error
cn.mops
4.4 years ago millerh1 ▴ 10
0
votes
1
reply
844
views
Error using singlecn.mops for cnv detection in WGS data
cnv cn.mops singlecn.mops
updated 2.1 years ago by • 0 • written 4.5 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 2.9 years ago by • 0 • written 4.8 years ago by • 0
0
votes
3
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954
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Error in if (all(x <= minReadCount) & lambda <= minReadCount) { : missing value where TRUE/FALSE needed
cnmops cn.mops error
updated 4.9 years ago by 25k • written 4.9 years ago by • 0
1
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4
replies
925
views
cn.mops on CRAM files
cn.mops
updated 4.9 years ago by ▴ 540 • written 4.9 years ago by • 0
2
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3
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1.2k
views
mosdepth output into cn.mops?
cn.mops
updated 5.1 years ago by ▴ 540 • written 5.1 years ago by • 0
0
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0
replies
654
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cn.mops normalization of multiple samples
cn.mops
5.2 years ago DannyM • 0
0
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3
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936
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tumor vs control: multiple samples
cn.mops
5.4 years ago • updated 5.3 years ago DannyM • 0
0
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0
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937
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Mean and median values in cn.mops cnvs output
cn.mops referencecn.mops
updated 5.3 years ago by 0 • written 5.4 years ago by • 0
0
votes
1
reply
962
views
cn.MOPS: Error in getReadCountsFromBAM
cn.mops
5.6 years ago laurabuggiotti • 0
0
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0
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948
views
Doubt about the interpretation of cn.mops tumor vs normal results
cn.mops dnaseq bioinformatics
5.7 years ago Cased • 0
0
votes
0
replies
661
views
How to interpret out of referencecn.mops
referencecn.mops cn.mops
5.7 years ago eddie.kaho.ho • 0
0
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18
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4.4k
views
cn.MOPs: Error in value[[3L]](cond) :
cn.mops
updated 5.8 years ago by ▴ 540 • written 5.8 years ago by • 0
2
votes
3
replies
1.5k
views
Doubt about WL in cn.mops
dnacopy dnaseq genomic cn.mops cnv
updated 5.8 years ago by ▴ 540 • written 5.8 years ago by • 0
0
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1
reply
872
views
cn.mops: interpreting output when returnPosterior=TRUE
cn.mops
updated 6.0 years ago by ▴ 540 • written 6.0 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 13 months ago by • 0 • written 6.1 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
6.2 years ago hugo.magalhaes ▴ 10
0
votes
1
reply
990
views
Inconsistent Warning: GRanges out of bounds
cn.mops granges trim Genomicranges-method
6.2 years ago znl207 • 0
0
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1
reply
951
views
Error with plotting with target sequencing data
cn.mops
updated 6.2 years ago by ▴ 540 • written 6.2 years ago by • 0
0
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5
replies
1.5k
views
Error when use getSegmentReadCountsFromBAM
targeted sequencing cn.mops
6.3 years ago jinxinhao1988 • 0
2
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6
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2.5k
views
Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error cn.mops
updated 6 weeks ago by • 0 • written 6.3 years ago by ▴ 10
0
votes
2
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1.4k
views
cn.MOPs issue with "Error in if (all(segMedianT == 0))"
cn.mops cnv
updated 6.4 years ago by ▴ 540 • written 6.4 years ago by ▴ 20
0
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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 6.4 years ago by ▴ 540 • written 6.4 years ago by • 0
5
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7
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1.5k
views
about the runs with cn.mops
cn.mops referencecn.mops
6.7 years ago • updated 6.6 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 6.8 years ago by ▴ 540 • written 6.8 years ago by • 0
0
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1
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1.0k
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getReadCountsFromBAM including bed information
cn.mops bed files getReadCountsFromBAM
6.8 years ago Pau Marc Muñoz Torres ▴ 20
5
votes
9
replies
1.8k
views
reduce function after combining 2 GRanges objects from cn.mops output
GRanges cn.mops
updated 6.8 years ago by ★ 11k • written 6.8 years ago by ▴ 110
2
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1
reply
1.0k
views
How to combine CNVDetectionResult objects in cn.mops package
cn.mops
updated 6.8 years ago by ▴ 540 • written 6.8 years ago by ▴ 110
4
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2
replies
1.4k
views
using cn.MOPS on WES data GERMLINE-TUMOR
cn.mops
6.9 years ago Bogdan ▴ 670
0
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2
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1.1k
views
getReadCountsFromBAM and paired-end reads
cn.mops
6.9 years ago Alexandre Kuhn ▴ 20
0
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2
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1.3k
views
Conflict in cnvr and cnvs result from cn.mops
cn.mops
updated 6.9 years ago by ▴ 540 • written 7.0 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 7.0 years ago by ▴ 540 • written 7.0 years ago by • 0
1
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1
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962
views
which cn.mops function should I use
cn.mops
updated 7.0 years ago by ▴ 540 • written 7.0 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 7.1 years ago by ▴ 540 • written 7.1 years ago by • 0
3
votes
1
reply
1.2k
views
R code for cn.mops -- if a chromosome does not have CNV ?
cn.mops referencecn.mops
updated 7.0 years ago by ▴ 540 • written 7.2 years ago by ▴ 670
3
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5
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1.5k
views
R code for cn.mops
cn.mops
updated 13 months ago by • 0 • written 7.2 years ago by ▴ 670
0
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2
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1.4k
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about an error in cn.MOPS : could not find symbol "recursive" in environment of the generic function
cn.MOPS
7.2 years ago Bogdan ▴ 670
0
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4
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1.4k
views
Call CNV in population with large depth variance
cn.mops
updated 7.3 years ago by ▴ 540 • written 7.3 years ago by • 0
4
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9
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2.3k
views
How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
cn.mops cnv targeted sequencing
updated 7.3 years ago by ▴ 540 • written 7.3 years ago by ▴ 20
0
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1
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844
views
Input (X) data type is not numeric if read from GRanges obj
cn.mops
updated 7.3 years ago by ▴ 540 • written 7.3 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 7.4 years ago by ▴ 540 • written 7.4 years ago by ▴ 90
0
votes
2
replies
1.1k
views
about cn.MOPS: paired vs unpaired
cn.mops
updated 7.5 years ago by ▴ 540 • written 7.5 years ago by ▴ 670
1
vote
1
reply
862
views
Suggestion: type of ExpLogFoldChange (sini)
cn.mops
updated 7.5 years ago by ▴ 540 • written 7.5 years ago by • 0
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Are you commenting on the OP's question, or adding a different question? If the latter, please start a new post rather than piggybacking on…
Answer: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Use `bquote`. See section 4.6 in [the vignette][1]. [1]: https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/in…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
I was thinking about removing unwanted variations at the sample level (ie a transformation shared across genes) not at the gene level. Corr…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
That's an assumption used for normalization of a sample, not an assumption you can use for an individual model. We always normalize to atte…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
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biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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