Showing : cn.mops • reset
2
votes
5
replies
1.4k
views
Error in referencecn.mops() for paired exome sequencing (normal/tumor)
cn.mops
updated 8.2 years ago by ▴ 540 • written 8.2 years ago by ▴ 10
2
votes
6
replies
2.5k
views
Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error cn.mops
updated 7 weeks ago by • 0 • written 6.3 years ago by ▴ 10
1
vote
7
replies
2.3k
views
Extracting CNV data from CNVDetectionResult
cn.mops
updated 8.4 years ago by ▴ 540 • written 8.8 years ago by • 0
0
votes
5
replies
1.4k
views
p or fdr values
cn.mops
8.7 years ago billnjcn • 0
3
votes
12
replies
2.4k
views
Error installing cn.mops and Rsamtools in R 3.1.3
rsamtools cn.mops installation
9.0 years ago Spollen, William G. ▴ 30
0
votes
4
replies
1.4k
views
No CNVs detected. Try changing "normalization", "priorImpact" or "thresholds".
No CNVs detected. Try changing "normalization" "priorImpact" or "thresholds". cn.mops
updated 7.6 years ago by ▴ 540 • written 7.6 years ago by • 0
0
votes
18
replies
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
0
votes
3
replies
1.8k
views
cn.mops CNV calling for multiple samples
cn.mops
updated 8.3 years ago by ▴ 540 • written 8.4 years ago by • 0
0
votes
5
replies
1.4k
views
Complete chromosome losses and polyploidies
cn.mops polyploidy
8.5 years ago mikko.arvas • 0
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
0
votes
3
replies
937
views
tumor vs control: multiple samples
cn.mops
5.4 years ago • updated 5.3 years ago DannyM • 0
0
votes
2
replies
1.1k
views
getReadCountsFromBAM and paired-end reads
cn.mops
6.9 years ago Alexandre Kuhn ▴ 20
5
votes
7
replies
1.5k
views
about the runs with cn.mops
cn.mops referencecn.mops
6.7 years ago • updated 6.6 years ago Bogdan ▴ 670
2
votes
8
replies
2.3k
views
Copy Number Variation in the cn.mops Package
cn.mops cnv cnvtools
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
2
votes
2
replies
1.2k
views
Save plot as png in cn.MOPS
cn.mops
8.3 years ago ashkot09 • 0
4
votes
3
replies
1.3k
views
parameter "refSeqName" in function "getReadCountsFromBAM"
cn.mops
updated 7.2 years ago by ▴ 540 • written 7.7 years ago by • 0
0
votes
4
replies
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
4
votes
2
replies
1.4k
views
using cn.MOPS on WES data GERMLINE-TUMOR
cn.mops
6.9 years ago Bogdan ▴ 670
0
votes
1
reply
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
4
votes
9
replies
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
votes
4
replies
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
3
votes
5
replies
1.5k
views
R code for cn.mops
cn.mops
updated 13 months ago by • 0 • written 7.2 years ago by ▴ 670
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
0
votes
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
1
vote
1
reply
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
votes
2
replies
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
2
votes
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
0
votes
1
reply
1.0k
views
getReadCountsFromBAM including bed information
cn.mops bed files getReadCountsFromBAM
6.8 years ago Pau Marc Muñoz Torres ▴ 20
1
vote
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
votes
4
replies
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
0
votes
2
replies
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
votes
5
replies
1.5k
views
Error when use getSegmentReadCountsFromBAM
targeted sequencing cn.mops
6.3 years ago jinxinhao1988 • 0
0
votes
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
votes
1
reply
1.2k
views
Detection copy number variations with cn.MOPS package
Coverage cn.mops Coverage cn.mops
updated 11.4 years ago by ▴ 540 • written 11.4 years ago by ▴ 50
0
votes
2
replies
1.7k
views
cn.mops: copy number for low-coverage bam files?
Sequencing Coverage cn.mops Sequencing Coverage cn.mops
updated 11.0 years ago by ▴ 540 • written 11.0 years ago by ▴ 750
1
vote
1
reply
1.1k
views
copy number segment calling with cn.mop when just one sample?
cn.mops cn.mops
updated 8.8 years ago by ▴ 540 • written 10.9 years ago by ▴ 750
0
votes
1
reply
1.4k
views
Negative Width error in cn.mops
cn.mops cn.mops
updated 8.8 years ago by ▴ 540 • written 10.6 years ago by ▴ 10
0
votes
1
reply
978
views
error in calculate integer copy numbers. bug?
cn.mops cn.mops
updated 10.2 years ago by ▴ 540 • written 10.2 years ago by ★ 13k
0
votes
1
reply
984
views
CNV detection using cn.farms for non-affymetrix arrays (custom oligonucleotide arrays)
Sequencing Microarray probe cn.mops Sequencing Microarray probe cn.mops
updated 10.1 years ago by ▴ 210 • written 10.1 years ago by ★ 13k
2
votes
2
replies
1.7k
views
Adjusting the defaults in the cn.MOPs Package
cn.mops cnv cnvtools
updated 8.8 years ago by ▴ 540 • written 8.8 years ago by • 0
1
vote
3
replies
1.7k
views
"Some normalization factors are zero" error on cn.mops
cn.mops
updated 8.7 years ago by ▴ 540 • written 8.7 years ago by ▴ 590
0
votes
1
reply
965
views
Unpaired CNV Exome
cn.mops
updated 8.7 years ago by ▴ 540 • written 8.7 years ago by • 0
0
votes
4
replies
1.9k
views
Using cn.MOPs to estimate CNVs in tumors without reference normal
cn.mops cnvtools tcga cnv
updated 8.5 years ago by ▴ 540 • written 8.5 years ago by ▴ 10
2
votes
6
replies
1.8k
views
refSeqName issue in cn.MOPS
CNV cn.mops
updated 8.3 years ago by ▴ 540 • written 8.3 years ago by • 0
0
votes
1
reply
999
views
cn.MOPS output file
cn.mops
updated 8.3 years ago by ▴ 540 • written 8.3 years ago by • 0
1
vote
4
replies
1.6k
views
Detect CNVs in target sample
CNV cn.mops
updated 8.3 years ago by ▴ 540 • written 8.3 years ago by • 0
0
votes
1
reply
873
views
problems on the CNV detection by cn.mops using multiply WGS data
cn.mops
updated 7.9 years ago by ▴ 540 • written 7.9 years ago by • 0
0
votes
2
replies
898
views
why there are multiple calls to cnmops C function?
cn.mops
updated 7.7 years ago by ▴ 540 • written 7.7 years ago by • 0
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
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
50 results • Page 1 of 1
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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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