Showing : Purecn • reset
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790
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Calculating tumour purity having only CNA data
PureCN CNA purity cancer
2.0 years ago JAcky • 0
1
vote
5
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1.7k
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Mutect version, matched normal and manual curation in PureCN
PureCN
2.1 years ago • updated 17 months ago Ken C • 0
1
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8
replies
1.6k
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PureCN: Copy Number of 7 issue
Pure PureCN
updated 2.6 years ago by ▴ 130 • written 2.6 years ago by • 0
1
vote
5
replies
1.4k
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PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 2.6 years ago by ▴ 130 • written 2.6 years ago by ▴ 10
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2
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1.0k
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PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 2.8 years ago by ▴ 130 • written 2.8 years ago by ▴ 10
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1
reply
765
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PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 2.9 years ago by ▴ 130 • written 2.9 years ago by ▴ 10
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3
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924
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Corrupt data in Sex column of .csv file
PureCN
3.2 years ago twtoal ▴ 10
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2
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1.3k
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PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
4.0 years ago twtoal ▴ 10
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3
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1.1k
views
PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 4.1 years ago by ▴ 130 • written 4.1 years ago by ▴ 10
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4
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1.0k
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Why is PureCN LOH file missing some segments
purecn loh
4.3 years ago twtoal ▴ 10
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1
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840
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PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 4.6 years ago by ▴ 130 • written 4.6 years ago by • 0
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2
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1.2k
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PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 4.6 years ago by ★ 6.5k • written 4.6 years ago by ▴ 10
0
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3
replies
957
views
callLOH output file NA values
PureCN NA values
updated 5.2 years ago by ▴ 130 • written 5.2 years ago by ▴ 10
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1
reply
1.1k
views
PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 5.2 years ago by ▴ 130 • written 5.2 years ago by ▴ 10
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1
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913
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Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
5.6 years ago twtoal ▴ 10
2
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5
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2.7k
views
Issue with BiocParallel
purecn biocparallel
5.7 years ago milos-91 • 0
0
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1
reply
913
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
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3
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1.2k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
5.7 years ago twtoal ▴ 10
0
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1
reply
1.1k
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
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2
replies
942
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Mutation Burden file and manual curation
purecn mutation_burden manual_curation
5.8 years ago twtoal ▴ 10
0
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1
reply
1.1k
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PureCN Solution Heatmap values
PureCN heatmap likelihoods
5.8 years ago twtoal ▴ 10
0
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2
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1.2k
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CNV in Normal Samples?
PureCN Germline Normal CNV
updated 5.8 years ago by ▴ 130 • written 5.8 years ago by ▴ 10
1
vote
1
reply
917
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
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1
reply
790
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
1
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3
replies
1.1k
views
PureCN Manual Curation .rds file
PureCN rds_file manual_curation
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
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4
replies
1.4k
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
votes
3
replies
1.9k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
6.0 years ago • updated 5.9 years ago twtoal ▴ 10
0
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1
reply
1.2k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
6.0 years ago twtoal ▴ 10
0
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6
replies
1.8k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
6.1 years ago skkujin • 0
0
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5
replies
1.9k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
3
votes
5
replies
1.7k
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Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 6.1 years ago by • 0 • written 6.3 years ago by ▴ 10
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1
reply
1.0k
views
Is C adjusted for purity?
PureCN Adjusted C
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
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9
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1.8k
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Unable to find solution: low coverage
PureCN fatal error no solution
6.1 years ago twtoal ▴ 10
0
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2
replies
906
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
0
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4
replies
1.3k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
6.1 years ago twtoal ▴ 10
0
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6
replies
1.3k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
6.1 years ago twtoal ▴ 10
0
votes
2
replies
1.4k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
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4
replies
1.2k
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN Somatic Mutations
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
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2
replies
967
views
Dx.R somatic_ontarget column
PureCN
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
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1
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1.0k
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
1
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3
replies
1000
views
PureCN Release Notes
PureCN Release
updated 6.2 years ago by 66k • written 6.2 years ago by ▴ 10
0
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1
reply
1.9k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
votes
3
replies
1.0k
views
PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
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4
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1.4k
views
PureCN error: zero-length 'labels' specified
PureCN
6.2 years ago twtoal ▴ 10
0
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1
reply
824
views
PureCN Panel of Normals contents
PureCN
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
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2
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1.0k
views
No CNAs or SNVs in results
PureCN
6.2 years ago twtoal ▴ 10
1
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1
reply
1.0k
views
PureCN support for indels
PureCN indels
updated 6.2 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
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9
replies
1.4k
views
errors in version 1.7.53
PureCN
updated 6.8 years ago by ▴ 130 • written 6.8 years ago by • 0
0
votes
1
reply
1.1k
views
errors in Purecn callLOH
PureCN
updated 6.8 years ago by ▴ 130 • written 6.8 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 7.1 years ago by ▴ 130 • written 7.1 years ago by • 0
50 results • Page 1 of 1
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Comment: limma comparison for small sample size and how to get covariance matrix by Gordon Smyth 51k
Your MDS plot is better than before, but you are still not following the recommendation for making for making such plots given in the limma…
Comment: Mapping Between GenBank ID's and Uniprot by James W. MacDonald 66k
Also, ``` > result <- mapUniProt( from = "EMBL-GenBank-DDBJ_CDS", to = "UniProtKB", query = c("ACF95883.1") ) > result From…
Comment: Mapping Between GenBank ID's and Uniprot by James W. MacDonald 66k
Ugh, here's the link https://www.uniprot.org/id-mapping/uniprotkb/dd08aa16774d98ef087dc3bd708582012bba49e2/overview?fields=accession%2Cre…
Answer: Mapping Between GenBank ID's and Uniprot by James W. MacDonald 66k
The input should be 'EMBL-GenBank-DDBJ_CDS", as that is a GenBank ID.
Answer: XCMS2 of orbitrap data by Elodie • 0
Hi, I have the same question, I have acquired MS2 data with PRM analysis and inclusion lists of several ions. I have a list of product ion…
Votes
Answer: EPIC array hg38 annotation?
Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
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