Showing : purecn • reset
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193
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Calculating tumour purity having only CNA data
PureCN CNA purity cancer
7 months ago JAcky • 0
0
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4
replies
417
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Mutect version, matched normal and manual curation in PureCN
PureCN
7 months ago Ken C • 0
1
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8
replies
753
views
PureCN: Copy Number of 7 issue
Pure PureCN
updated 14 months ago by ▴ 120 • written 14 months ago by • 0
1
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5
replies
710
views
PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 14 months ago by ▴ 120 • written 14 months ago by ▴ 10
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2
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524
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PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 16 months ago by ▴ 120 • written 17 months ago by ▴ 10
0
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1
reply
378
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PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 17 months ago by ▴ 120 • written 17 months ago by ▴ 10
0
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3
replies
442
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Corrupt data in Sex column of .csv file
PureCN
21 months ago twtoal ▴ 10
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2
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626
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PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
2.6 years ago twtoal ▴ 10
0
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3
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523
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PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 2.7 years ago by ▴ 120 • written 2.7 years ago by ▴ 10
0
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4
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510
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Why is PureCN LOH file missing some segments
purecn loh
2.9 years ago twtoal ▴ 10
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1
reply
408
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PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 3.1 years ago by ▴ 120 • written 3.1 years ago by • 0
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2
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743
views
PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 3.2 years ago by ★ 5.9k • written 3.2 years ago by ▴ 10
0
votes
3
replies
520
views
callLOH output file NA values
PureCN NA values
updated 3.7 years ago by ▴ 120 • written 3.7 years ago by ▴ 10
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1
reply
514
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PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 3.8 years ago by ▴ 120 • written 3.8 years ago by ▴ 10
0
votes
1
reply
598
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Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
4.2 years ago twtoal ▴ 10
2
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5
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1.7k
views
Issue with BiocParallel
purecn biocparallel
4.3 years ago milos-91 • 0
0
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1
reply
526
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 4.3 years ago by ▴ 120 • written 4.3 years ago by ▴ 10
0
votes
3
replies
622
views
Assigning DUP/DEL p-value to CNV segment
PureCN
4.3 years ago twtoal ▴ 10
0
votes
1
reply
661
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 4.3 years ago by ▴ 120 • written 4.3 years ago by ▴ 10
0
votes
2
replies
543
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Mutation Burden file and manual curation
purecn mutation_burden manual_curation
4.3 years ago twtoal ▴ 10
0
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1
reply
575
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
4.3 years ago twtoal ▴ 10
0
votes
2
replies
641
views
CNV in Normal Samples?
PureCN Germline Normal CNV
updated 4.4 years ago by ▴ 120 • written 4.4 years ago by ▴ 10
1
vote
1
reply
566
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 4.4 years ago by ▴ 120 • written 4.4 years ago by ▴ 10
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votes
1
reply
443
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 4.4 years ago by ▴ 120 • written 4.4 years ago by ▴ 10
1
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3
replies
596
views
PureCN Manual Curation .rds file
PureCN rds_file manual_curation
updated 4.4 years ago by ▴ 120 • written 4.4 years ago by ▴ 10
0
votes
4
replies
897
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 4.5 years ago by ▴ 120 • written 4.5 years ago by ▴ 10
0
votes
3
replies
1.4k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
4.6 years ago • updated 4.5 years ago twtoal ▴ 10
0
votes
1
reply
741
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
4.6 years ago twtoal ▴ 10
0
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6
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1.1k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
4.7 years ago skkujin • 0
0
votes
5
replies
1.1k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 4.7 years ago by ▴ 120 • written 4.7 years ago by ▴ 10
0
votes
1
reply
570
views
Is C adjusted for purity?
PureCN Adjusted C
updated 4.7 years ago by ▴ 120 • written 4.7 years ago by ▴ 10
0
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9
replies
949
views
Unable to find solution: low coverage
PureCN fatal error no solution
4.7 years ago twtoal ▴ 10
0
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2
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554
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PureCN removemapq0 parameter
PureCN removemapq0
updated 4.7 years ago by ▴ 120 • written 4.7 years ago by ▴ 10
0
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4
replies
760
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
4.7 years ago twtoal ▴ 10
0
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6
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770
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
4.7 years ago twtoal ▴ 10
0
votes
2
replies
765
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 4.7 years ago by ▴ 120 • written 4.7 years ago by ▴ 10
0
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4
replies
647
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN Somatic Mutations
updated 4.8 years ago by ▴ 120 • written 4.8 years ago by ▴ 10
0
votes
2
replies
530
views
Dx.R somatic_ontarget column
PureCN
updated 4.8 years ago by ▴ 120 • written 4.8 years ago by ▴ 10
0
votes
1
reply
625
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 4.8 years ago by ▴ 120 • written 4.8 years ago by ▴ 10
1
vote
3
replies
610
views
PureCN Release Notes
PureCN Release
updated 4.8 years ago by 62k • written 4.8 years ago by ▴ 10
0
votes
1
reply
1.4k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 4.8 years ago by ▴ 120 • written 4.8 years ago by ▴ 10
0
votes
3
replies
574
views
PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 4.8 years ago by ▴ 120 • written 4.8 years ago by ▴ 10
0
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4
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804
views
PureCN error: zero-length 'labels' specified
PureCN
4.8 years ago twtoal ▴ 10
0
votes
1
reply
452
views
PureCN Panel of Normals contents
PureCN
updated 4.8 years ago by ▴ 120 • written 4.8 years ago by ▴ 10
0
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2
replies
571
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No CNAs or SNVs in results
PureCN
4.8 years ago twtoal ▴ 10
3
votes
5
replies
1.1k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 4.7 years ago by • 0 • written 4.8 years ago by ▴ 10
1
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1
reply
581
views
PureCN support for indels
PureCN indels
updated 4.8 years ago by ▴ 120 • written 4.8 years ago by ▴ 10
0
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9
replies
737
views
errors in version 1.7.53
PureCN
updated 5.3 years ago by ▴ 120 • written 5.3 years ago by • 0
0
votes
1
reply
684
views
errors in Purecn callLOH
PureCN
updated 5.3 years ago by ▴ 120 • written 5.3 years ago by • 0
2
votes
3
replies
813
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PureCN can classify indel variants as germline vs. somatic ?
PureCN indel somatic germline
updated 5.7 years ago by ▴ 120 • written 5.7 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Not able to download recount3 data by Niveditha ▴ 10
Thank you for the update, Leo. I'll check on this and get back to you in case the issue still persists.
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE by Hervé Pagès 16k
See https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE by Hervé Pagès 16k
See https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932
Comment: Sva and batch effect by Gordon Smyth 47k
(+1). I find that ComBat tends to introduce spurious differential expression so, you think there's a batch effect affecting the variances a…
Comment: Advice for the analysis of microarray data with limma by Gordon Smyth 47k
You mean references on orthogonal polynomials? Polynomial approximation is a classic topic in mathematics and statistics and there are many…
Votes
Answer: Sva and batch effect
Answer: AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Answer: Limma-voom with inverse probability weights
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Scholar to James W. MacDonald 62k
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