Showing : purecn • reset
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729
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Calculating tumour purity having only CNA data
PureCN CNA purity cancer
22 months ago JAcky • 0
1
vote
5
replies
1.5k
views
Mutect version, matched normal and manual curation in PureCN
PureCN
22 months ago • updated 14 months ago Ken C • 0
1
vote
8
replies
1.5k
views
PureCN: Copy Number of 7 issue
Pure PureCN
updated 2.4 years ago by ▴ 130 • written 2.4 years ago by • 0
1
vote
5
replies
1.3k
views
PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 2.4 years ago by ▴ 130 • written 2.4 years ago by ▴ 10
0
votes
2
replies
979
views
PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 2.6 years ago by ▴ 130 • written 2.6 years ago by ▴ 10
0
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1
reply
692
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PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 2.7 years ago by ▴ 130 • written 2.7 years ago by ▴ 10
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3
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861
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Corrupt data in Sex column of .csv file
PureCN
3.0 years ago twtoal ▴ 10
0
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2
replies
1.1k
views
PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
3.8 years ago twtoal ▴ 10
0
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3
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1.0k
views
PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 4.0 years ago by ▴ 130 • written 4.0 years ago by ▴ 10
0
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4
replies
964
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Why is PureCN LOH file missing some segments
purecn loh
4.1 years ago twtoal ▴ 10
0
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1
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788
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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
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2
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1.1k
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PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 4.4 years ago by ★ 6.5k • written 4.4 years ago by ▴ 10
0
votes
3
replies
900
views
callLOH output file NA values
PureCN NA values
updated 5.0 years ago by ▴ 130 • written 5.0 years ago by ▴ 10
0
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1
reply
1.0k
views
PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 5.0 years ago by ▴ 130 • written 5.0 years ago by ▴ 10
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1
reply
871
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
5.4 years ago twtoal ▴ 10
2
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5
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2.5k
views
Issue with BiocParallel
purecn biocparallel
5.5 years ago milos-91 • 0
0
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1
reply
869
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 5.5 years ago by ▴ 130 • written 5.5 years ago by ▴ 10
0
votes
3
replies
1.1k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
5.5 years ago twtoal ▴ 10
0
votes
1
reply
1000
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 5.5 years ago by ▴ 130 • written 5.5 years ago by ▴ 10
0
votes
2
replies
897
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
5.6 years ago twtoal ▴ 10
0
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1
reply
1.0k
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PureCN Solution Heatmap values
PureCN heatmap likelihoods
5.6 years ago twtoal ▴ 10
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
1
vote
1
reply
862
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
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1
reply
742
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
1
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3
replies
1.0k
views
PureCN Manual Curation .rds file
PureCN rds_file manual_curation
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
votes
4
replies
1.3k
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
votes
3
replies
1.8k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
5.8 years ago • updated 5.7 years ago twtoal ▴ 10
0
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1
reply
1.1k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
5.8 years ago twtoal ▴ 10
0
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6
replies
1.7k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
5.9 years ago skkujin • 0
0
votes
5
replies
1.8k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
3
votes
5
replies
1.6k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 5.9 years ago by • 0 • written 6.1 years ago by ▴ 10
0
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1
reply
954
views
Is C adjusted for purity?
PureCN Adjusted C
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
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9
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1.6k
views
Unable to find solution: low coverage
PureCN fatal error no solution
5.9 years ago twtoal ▴ 10
0
votes
2
replies
867
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
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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
6
replies
1.3k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
5.9 years ago twtoal ▴ 10
0
votes
2
replies
1.3k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
4
replies
1.2k
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN Somatic Mutations
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
2
replies
907
views
Dx.R somatic_ontarget column
PureCN
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
1
reply
980
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
1
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3
replies
943
views
PureCN Release Notes
PureCN Release
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 10
0
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1
reply
1.8k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
3
replies
970
views
PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
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4
replies
1.3k
views
PureCN error: zero-length 'labels' specified
PureCN
6.0 years ago twtoal ▴ 10
0
votes
1
reply
776
views
PureCN Panel of Normals contents
PureCN
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
2
replies
976
views
No CNAs or SNVs in results
PureCN
6.0 years ago twtoal ▴ 10
1
vote
1
reply
941
views
PureCN support for indels
PureCN indels
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
0
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9
replies
1.4k
views
errors in version 1.7.53
PureCN
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by • 0
0
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1
reply
1.1k
views
errors in Purecn callLOH
PureCN
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by • 0
2
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3
replies
1.2k
views
PureCN can classify indel variants as germline vs. somatic ?
PureCN indel somatic germline
updated 6.9 years ago by ▴ 130 • written 6.9 years ago by • 0
50 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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