Showing : cnv • reset
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
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
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
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
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
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
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
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
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
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
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
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
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
1
reply
1.4k
views
ExomeDepth Package Error Messages
cnv exome
8.2 years ago Bio152 ▴ 150
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
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
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
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
4
replies
1.3k
views
CNV caller software
CNV
7.6 years ago Bogdan ▴ 670
0
votes
0
replies
1.3k
views
'GenomeInfoDb' error in the cn.MOPS Package
cnv genomeinfodb
8.8 years ago voksdvoks • 0
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
1.2k
views
exomeCopy copy number setting
cnv exomecopy
updated 8.4 years ago by 41k • written 8.4 years ago by ▴ 20
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
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
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
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
1
reply
1.1k
views
NGScopy package throwing error during installation
NGScopy installation CNV
8.7 years ago JstRoRR • 0
1
vote
2
replies
1.0k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks cnv
2.5 years ago raf4 ▴ 20
0
votes
3
replies
1.0k
views
exomeCopy error with compileCopyCountSegments
exomecopy cnv
6.3 years ago ramakrishnas • 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
963
views
how to analyze "Beta-score" and get CNVdata using Comunee
conumee CNV 450K
6.2 years ago bird.of.clockwise • 0
3
votes
2
replies
957
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
0
votes
2
replies
933
views
Filter CNVs if contain certain gene
cnv genomic ranges cnvs
6.8 years ago julrodr80 ▴ 30
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
0
votes
0
replies
871
views
Noise Analyses of CNV Data from TCGA
tcgabiolinks tcga cnv noise pruning
5.8 years ago jrlarsen ▴ 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
votes
0
replies
825
views
visualize CNV data based on WGS
CNV
6.3 years ago Bogdan ▴ 670
0
votes
1
reply
788
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
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
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
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
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
554
views
ExomeDepth package- error with "select.reference.set" function
ExomeDepth CNV
4.4 years ago Bouzid.a ▴ 20
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
45 results • Page 1 of 1
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Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
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?
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