Showing : cnv • reset
1
vote
5
replies
1.6k
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
8.2 years ago IOM ▴ 20
4
votes
13
replies
3.3k
views
Gaia not returning results - load_cnv problem
gaia cnv
updated 2.6 years ago by • 0 • written 5.7 years ago by ▴ 30
0
votes
4
replies
1.4k
views
Trouble following the first 5 lines of vanillaICE tutorial?
SNP6 crlmm vanillaice vanillaice crlmm cnv
updated 8.9 years ago by • 0 • written 8.9 years ago by ▴ 20
7
votes
9
replies
1.6k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq CNV TCGA450KHumanMethylationCalibrationDataset qsea PRAD
2.9 years ago rtrivedi1 ▴ 10
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
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
3
replies
1.5k
views
Mapping of two different regions to one gene symbol
TCGA CNV
updated 8.9 years ago by ★ 7.2k • written 8.9 years ago by ▴ 60
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
1.4k
views
Error: could not find function "readGVF"
GVF CNV cnvGSA
updated 8.5 years ago by 65k • written 8.5 years ago by ▴ 40
0
votes
1
reply
1.2k
views
exomeCopy copy number setting
cnv exomecopy
updated 8.4 years ago by 41k • written 8.4 years ago by ▴ 20
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
1.5k
views
CopywriteR: CNV calling on normals samples / gaps in chromosomes
copynumber cnvtools cnv copywriteR
updated 7.7 years ago by ▴ 170 • written 7.7 years ago by • 0
0
votes
4
replies
1.3k
views
CNV caller software
CNV
7.6 years ago Bogdan ▴ 670
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
2
votes
2
replies
1.3k
views
detecting of CNV in WGS/WES data
CNV WGS WES
updated 6.8 years ago by ▴ 110 • written 6.8 years ago by ▴ 670
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
3
replies
1.0k
views
exomeCopy error with compileCopyCountSegments
exomecopy cnv
6.3 years ago ramakrishnas • 0
3
votes
2
replies
956
views
counting the sequencing reads in 10kb regions on a genome-wide scale
read counting CNV rsamtools
updated 6.1 years ago by 65k • written 6.1 years ago by ▴ 670
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
votes
2
replies
2.5k
views
Error: vector memory exhausted (limit reached?)
tcgabiolinks tcga cnv mac os x gaia
updated 5.7 years ago by ▴ 20 • written 5.7 years ago by ▴ 30
0
votes
2
replies
1.1k
views
CNV in Normal Samples?
PureCN Germline Normal CNV
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
votes
1
reply
786
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 4.4 years ago by ▴ 130 • written 4.4 years ago by • 0
2
votes
4
replies
878
views
CopywriteR job runs out of memory
copywriter cnv
updated 4.0 years ago by ▴ 20 • written 4.0 years ago by ▴ 190
1
vote
2
replies
1.0k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks cnv
2.5 years ago raf4 ▴ 20
0
votes
0
replies
567
views
Applying exomeCopy to call CNVs withouts controls considering batch effects
exomeCopy CNV WES
3.1 years ago Cheng • 0
0
votes
0
replies
825
views
visualize CNV data based on WGS
CNV
6.3 years ago Bogdan ▴ 670
0
votes
0
replies
962
views
how to analyze "Beta-score" and get CNVdata using Comunee
conumee CNV 450K
6.2 years ago bird.of.clockwise • 0
0
votes
0
replies
742
views
cn.MOPS output - mean/median of what?
cn.MOPS CNV copy number
4.2 years ago liorglic ▴ 10
0
votes
4
replies
1.2k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
5.9 years ago twtoal ▴ 10
0
votes
0
replies
870
views
Noise Analyses of CNV Data from TCGA
tcgabiolinks tcga cnv noise pruning
5.8 years ago jrlarsen ▴ 10
0
votes
1
reply
718
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
4.1 years ago metzgerlukas • 0
0
votes
1
reply
1.1k
views
NGScopy package throwing error during installation
NGScopy installation CNV
8.7 years ago JstRoRR • 0
0
votes
0
replies
462
views
cn.mops : undef chromsome using data matrix as input
CNV cn.mops undef
4.1 years ago ankita.narang86 • 0
0
votes
0
replies
1.3k
views
'GenomeInfoDb' error in the cn.MOPS Package
cnv genomeinfodb
8.8 years ago voksdvoks • 0
0
votes
1
reply
1.4k
views
ExomeDepth Package Error Messages
cnv exome
8.2 years ago Bio152 ▴ 150
0
votes
2
replies
3.3k
views
Pipeline for analyzing CNV (SNP array) level 3 from TCGA
SNP CNV TCGA
9.0 years ago NS ▴ 60
0
votes
0
replies
1.2k
views
crlmm: Does it support Illumina BeadChip platform HumanCore-24v1-0_A
cnv cnvtools crlmm
7.7 years ago enriquev • 0
0
votes
1
reply
968
views
Union of GenomicRanges problem when one range is empty
genomicranges R cnv
7.7 years ago WouterDeCoster ▴ 130
0
votes
0
replies
1.4k
views
DNAcopy default settings and SNP6.0 arrays
SNP DNAcopy SNP6.0 CNV
9.3 years ago giovanni.dario • 0
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
votes
0
replies
1.2k
views
DNA methylation 450k data - minfi - preprocessFunnorm - CNV cases vs non-CNV controls
CNV minfi preprocessing dna methylation
7.1 years ago Thomas • 0
2
votes
2
replies
1.1k
views
list fo genes by cnv
cnv genes genomic ranges splitByOverlap
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 30
0
votes
2
replies
933
views
Filter CNVs if contain certain gene
cnv genomic ranges cnvs
6.8 years ago julrodr80 ▴ 30
0
votes
0
replies
554
views
ExomeDepth package- error with "select.reference.set" function
ExomeDepth CNV
4.4 years ago Bouzid.a ▴ 20
0
votes
1
reply
762
views
CNV plot using cn.mops
cnv R plot visualization cn.mops software error
4.4 years ago ari • 0
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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