Showing : PureCN • reset
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4
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BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN biomaRt
updated 11 weeks ago by • 0 • written 5 months ago by • 0
0
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0
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969
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Calculating tumour purity having only CNA data
PureCN CNA purity cancer
2.6 years ago JAcky • 0
1
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5
replies
2.1k
views
Mutect version, matched normal and manual curation in PureCN
PureCN
2.6 years ago • updated 24 months ago Ken C • 0
1
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8
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1.9k
views
PureCN: Copy Number of 7 issue
Pure PureCN
updated 3.2 years ago by ▴ 130 • written 3.2 years ago by • 0
1
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5
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1.8k
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PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 3.2 years ago by ▴ 130 • written 3.2 years ago by ▴ 10
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2
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1.3k
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PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 3.4 years ago by ▴ 130 • written 3.4 years ago by ▴ 10
0
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1
reply
923
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PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 3.5 years ago by ▴ 130 • written 3.5 years ago by ▴ 10
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3
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1.1k
views
Corrupt data in Sex column of .csv file
PureCN
3.7 years ago twtoal ▴ 10
0
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2
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1.6k
views
PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
4.6 years ago twtoal ▴ 10
0
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3
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1.4k
views
PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 4.7 years ago by ▴ 130 • written 4.7 years ago by ▴ 10
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4
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1.3k
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Why is PureCN LOH file missing some segments
purecn loh
4.9 years ago twtoal ▴ 10
0
votes
1
reply
995
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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2
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1.4k
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PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 5.2 years ago by ★ 6.6k • written 5.2 years ago by ▴ 10
0
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3
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1.2k
views
callLOH output file NA values
PureCN NA values
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
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1
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1.3k
views
PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 5.7 years ago by ▴ 130 • written 5.8 years ago by ▴ 10
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1
reply
1.0k
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
6.2 years ago twtoal ▴ 10
2
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5
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3.0k
views
Issue with BiocParallel
purecn biocparallel
6.3 years ago milos-91 • 0
0
votes
1
reply
1.1k
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
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3
replies
1.4k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
6.3 years ago twtoal ▴ 10
0
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1
reply
1.2k
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
6.3 years ago twtoal ▴ 10
0
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1
reply
1.2k
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
6.3 years ago twtoal ▴ 10
0
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2
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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
1
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1
reply
1.1k
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 6.4 years ago by ▴ 130 • written 6.4 years ago by ▴ 10
0
votes
1
reply
935
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 6.4 years ago by ▴ 130 • written 6.4 years ago by ▴ 10
1
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3
replies
1.3k
views
PureCN Manual Curation .rds file
PureCN rds_file manual_curation
updated 6.4 years ago by ▴ 130 • written 6.4 years ago by ▴ 10
0
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4
replies
1.7k
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 6.4 years ago by ▴ 130 • written 6.4 years ago by ▴ 10
0
votes
3
replies
2.2k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
6.6 years ago • updated 6.5 years ago twtoal ▴ 10
0
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1
reply
1.4k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
6.6 years ago twtoal ▴ 10
0
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6
replies
2.1k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
6.6 years ago skkujin • 0
0
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5
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2.1k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
3
votes
5
replies
2.0k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 6.7 years ago by • 0 • written 6.8 years ago by ▴ 10
0
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1
reply
1.2k
views
Is C adjusted for purity?
PureCN Adjusted C
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
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9
replies
2.2k
views
Unable to find solution: low coverage
PureCN fatal error no solution
6.7 years ago twtoal ▴ 10
0
votes
2
replies
1.0k
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
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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
0
votes
6
replies
1.6k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
6.7 years ago twtoal ▴ 10
0
votes
2
replies
1.6k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
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4
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1.5k
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN Somatic Mutations
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
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2
replies
1.2k
views
Dx.R somatic_ontarget column
PureCN
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
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1
reply
1.2k
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
1
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3
replies
1.2k
views
PureCN Release Notes
PureCN Release
updated 6.8 years ago by 67k • written 6.8 years ago by ▴ 10
0
votes
1
reply
2.1k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 6.8 years ago by ▴ 130 • written 6.8 years ago by ▴ 10
0
votes
3
replies
1.2k
views
PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 6.8 years ago by ▴ 130 • written 6.8 years ago by ▴ 10
0
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4
replies
1.6k
views
PureCN error: zero-length 'labels' specified
PureCN
6.8 years ago twtoal ▴ 10
0
votes
1
reply
957
views
PureCN Panel of Normals contents
PureCN
updated 6.8 years ago by ▴ 130 • written 6.8 years ago by ▴ 10
0
votes
2
replies
1.2k
views
No CNAs or SNVs in results
PureCN
6.8 years ago twtoal ▴ 10
1
vote
1
reply
1.2k
views
PureCN support for indels
PureCN indels
updated 6.8 years ago by ▴ 130 • written 6.8 years ago by ▴ 10
0
votes
9
replies
1.7k
views
errors in version 1.7.53
PureCN
updated 7.3 years ago by ▴ 130 • written 7.3 years ago by • 0
0
votes
1
reply
1.3k
views
errors in Purecn callLOH
PureCN
updated 7.3 years ago by ▴ 130 • written 7.3 years ago by • 0
50 results • Page 1 of 1
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Answer: Selection of correct coefficients or contrasts in DESeq2 by swbarnes2 ★ 1.4k
I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…
Comment: Csaw normalization strategies - general inquiry by Luca • 0
Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by Quang NN ▴ 10
Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …
Answer: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by ATpoint ★ 4.6k
My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …
Votes
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
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