Showing : CNV • reset
1
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2
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1.4k
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Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks cnv
3.3 years ago • updated 3.2 years ago raf4 ▴ 30
7
votes
9
replies
2.0k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq CNV TCGA450KHumanMethylationCalibrationDataset qsea PRAD
3.7 years ago • updated 3.6 years ago rtrivedi1 ▴ 10
0
votes
0
replies
718
views
Applying exomeCopy to call CNVs withouts controls considering batch effects
exomeCopy CNV WES
3.8 years ago Cheng • 0
4
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13
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3.9k
views
Gaia not returning results - load_cnv problem
gaia cnv
updated 3.4 years ago by • 0 • written 6.4 years ago by ▴ 30
2
votes
4
replies
1.1k
views
CopywriteR job runs out of memory
copywriter cnv
updated 4.7 years ago by ▴ 20 • written 4.7 years ago by ▴ 220
0
votes
1
reply
872
views
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
4.9 years ago metzgerlukas • 0
0
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0
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621
views
cn.mops : undef chromsome using data matrix as input
CNV cn.mops undef
4.9 years ago ankita.narang86 • 0
0
votes
0
replies
899
views
cn.MOPS output - mean/median of what?
cn.MOPS CNV copy number
4.9 years ago liorglic ▴ 10
0
votes
1
reply
992
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 5.1 years ago by ▴ 130 • written 5.1 years ago by • 0
0
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1
reply
948
views
CNV plot using cn.mops
cnv R plot visualization cn.mops software error
5.1 years ago ari • 0
0
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0
replies
762
views
ExomeDepth package- error with "select.reference.set" function
ExomeDepth CNV
5.1 years ago Bouzid.a ▴ 20
0
votes
1
reply
1.0k
views
Error using singlecn.mops for cnv detection in WGS data
cnv cn.mops singlecn.mops
updated 2.9 years ago by • 0 • written 5.2 years ago by • 0
0
votes
2
replies
1.4k
views
CNV in Normal Samples?
PureCN Germline Normal CNV
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
votes
2
replies
2.9k
views
Error: vector memory exhausted (limit reached?)
tcgabiolinks tcga cnv mac os x gaia
updated 6.5 years ago by ▴ 20 • written 6.5 years ago by ▴ 30
2
votes
3
replies
1.8k
views
Doubt about WL in cn.mops
dnacopy dnaseq genomic cn.mops cnv
updated 6.6 years ago by ▴ 540 • written 6.6 years ago by • 0
0
votes
0
replies
1.1k
views
Noise Analyses of CNV Data from TCGA
tcgabiolinks tcga cnv noise pruning
6.6 years ago jrlarsen ▴ 10
0
votes
4
replies
1.5k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
6.7 years ago twtoal ▴ 10
3
votes
2
replies
1.1k
views
counting the sequencing reads in 10kb regions on a genome-wide scale
read counting CNV rsamtools
updated 6.9 years ago by 67k • written 6.9 years ago by ▴ 670
0
votes
0
replies
1.2k
views
how to analyze "Beta-score" and get CNVdata using Comunee
conumee CNV 450K
6.9 years ago bird.of.clockwise • 0
0
votes
0
replies
980
views
visualize CNV data based on WGS
CNV
7.0 years ago Bogdan ▴ 670
0
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3
replies
1.2k
views
exomeCopy error with compileCopyCountSegments
exomecopy cnv
7.0 years ago ramakrishnas • 0
0
votes
2
replies
1.7k
views
cn.MOPs issue with "Error in if (all(segMedianT == 0))"
cn.mops cnv
updated 7.1 years ago by ▴ 540 • written 7.1 years ago by ▴ 20
2
votes
2
replies
1.6k
views
detecting of CNV in WGS/WES data
CNV WGS WES
updated 7.5 years ago by ▴ 110 • written 7.5 years ago by ▴ 670
0
votes
2
replies
1.1k
views
Filter CNVs if contain certain gene
cnv genomic ranges cnvs
7.6 years ago julrodr80 ▴ 30
2
votes
2
replies
1.2k
views
list fo genes by cnv
cnv genes genomic ranges splitByOverlap
updated 7.8 years ago by 25k • written 7.8 years ago by ▴ 30
0
votes
0
replies
1.4k
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DNA methylation 450k data - minfi - preprocessFunnorm - CNV cases vs non-CNV controls
CNV minfi preprocessing dna methylation
7.8 years ago Thomas • 0
4
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9
replies
2.7k
views
How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
cn.mops cnv targeted sequencing
updated 8.0 years ago by ▴ 540 • written 8.0 years ago by ▴ 20
0
votes
4
replies
1.5k
views
CNV caller software
CNV
8.3 years ago Bogdan ▴ 670
0
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1
reply
1.2k
views
Union of GenomicRanges problem when one range is empty
genomicranges R cnv
8.5 years ago WouterDeCoster ▴ 130
0
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0
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1.4k
views
crlmm: Does it support Illumina BeadChip platform HumanCore-24v1-0_A
cnv cnvtools crlmm
8.5 years ago enriquev • 0
0
votes
1
reply
1.9k
views
CopywriteR: CNV calling on normals samples / gaps in chromosomes
copynumber cnvtools cnv copywriteR
updated 8.5 years ago by ▴ 170 • written 8.5 years ago by • 0
0
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1
reply
1.7k
views
ExomeDepth Package Error Messages
cnv exome
8.9 years ago Bio152 ▴ 150
1
vote
5
replies
1.8k
views
Is there any way of exporting CNV data from Affymetrix SNP 6.0 arrays from Nexus Software for OncoScan?
cnv nexus for oncoscan Affymetrix 6.0 .BGR
9.0 years ago IOM ▴ 20
1
vote
4
replies
1.8k
views
Detect CNVs in target sample
CNV cn.mops
updated 9.0 years ago by ▴ 540 • written 9.0 years ago by • 0
2
votes
6
replies
2.0k
views
refSeqName issue in cn.MOPS
CNV cn.mops
updated 9.1 years ago by ▴ 540 • written 9.1 years ago by • 0
0
votes
1
reply
1.4k
views
exomeCopy copy number setting
cnv exomecopy
updated 9.2 years ago by 43k • written 9.2 years ago by ▴ 20
1
vote
3
replies
1.5k
views
Error: could not find function "readGVF"
GVF CNV cnvGSA
updated 9.2 years ago by 67k • written 9.2 years ago by ▴ 40
0
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1
reply
1.3k
views
NGScopy package throwing error during installation
NGScopy installation CNV
9.5 years ago JstRoRR • 0
2
votes
2
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2.0k
views
Adjusting the defaults in the cn.MOPs Package
cn.mops cnv cnvtools
updated 9.5 years ago by ▴ 540 • written 9.5 years ago by • 0
2
votes
8
replies
2.7k
views
Copy Number Variation in the cn.mops Package
cn.mops cnv cnvtools
updated 9.5 years ago by 25k • written 9.5 years ago by • 0
0
votes
0
replies
1.4k
views
'GenomeInfoDb' error in the cn.MOPS Package
cnv genomeinfodb
9.5 years ago voksdvoks • 0
0
votes
3
replies
1.7k
views
Mapping of two different regions to one gene symbol
TCGA CNV
updated 9.7 years ago by ★ 7.2k • written 9.7 years ago by ▴ 60
0
votes
4
replies
1.6k
views
Trouble following the first 5 lines of vanillaICE tutorial?
SNP6 crlmm vanillaice vanillaice crlmm cnv
updated 9.7 years ago by • 0 • written 9.7 years ago by ▴ 20
0
votes
2
replies
3.5k
views
Pipeline for analyzing CNV (SNP array) level 3 from TCGA
SNP CNV TCGA
9.7 years ago NS ▴ 60
0
votes
0
replies
1.6k
views
DNAcopy default settings and SNP6.0 arrays
SNP DNAcopy SNP6.0 CNV
10.0 years ago giovanni.dario • 0
45 results • Page 1 of 1
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Replies
Comment: How can I generate a heatmap and clustering of differentially expressed genes in by Renuka • 0
Thanks Kelvin i had same doubt .Do i need to do log2 (FPKMcounts) for this
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Michael, Thank you very much!
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
Yes, with the knowledge that, it is expected to be underpowered.
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Thank you, Michael. How? Could you provide more details? Can I just do it as usual, I mean to include batch in the model?
Answer: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
The short answer is yes, you can use even a single sample to estimate the batch effect (and therefore control for it in otherwise confounde…
Votes
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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