Showing : purecn • reset
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Calculating tumour purity having only CNA data
PureCN CNA purity cancer
2.1 years ago JAcky • 0
1
vote
5
replies
1.7k
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Mutect version, matched normal and manual curation in PureCN
PureCN
2.1 years ago • updated 18 months ago Ken C • 0
1
vote
8
replies
1.7k
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PureCN: Copy Number of 7 issue
Pure PureCN
updated 2.7 years ago by ▴ 130 • written 2.7 years ago by • 0
1
vote
5
replies
1.5k
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PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 2.7 years ago by ▴ 130 • written 2.7 years ago by ▴ 10
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2
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1.1k
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PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 2.9 years ago by ▴ 130 • written 2.9 years ago by ▴ 10
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1
reply
787
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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 3.0 years ago by ▴ 10
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3
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954
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Corrupt data in Sex column of .csv file
PureCN
3.2 years ago twtoal ▴ 10
0
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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
4.1 years ago twtoal ▴ 10
0
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3
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1.2k
views
PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 4.2 years ago by ▴ 130 • written 4.2 years ago by ▴ 10
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4
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1.1k
views
Why is PureCN LOH file missing some segments
purecn loh
4.4 years ago twtoal ▴ 10
0
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1
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862
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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
0
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2
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1.2k
views
PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 4.7 years ago by ★ 6.5k • written 4.7 years ago by ▴ 10
0
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3
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1.0k
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callLOH output file NA values
PureCN NA values
updated 5.2 years ago by ▴ 130 • written 5.2 years ago by ▴ 10
0
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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
reply
933
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
5.7 years ago twtoal ▴ 10
2
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5
replies
2.7k
views
Issue with BiocParallel
purecn biocparallel
5.8 years ago milos-91 • 0
0
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1
reply
935
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 5.8 years ago by ▴ 130 • written 5.8 years ago by ▴ 10
0
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3
replies
1.2k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
5.8 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 5.8 years ago by ▴ 130 • written 5.8 years ago by ▴ 10
0
votes
2
replies
971
views
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
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
5.8 years ago twtoal ▴ 10
0
votes
2
replies
1.2k
views
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
933
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
votes
1
reply
813
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
0
votes
4
replies
1.5k
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
6.1 years ago • updated 6.0 years ago twtoal ▴ 10
0
votes
1
reply
1.2k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
6.1 years ago twtoal ▴ 10
0
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6
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1.8k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
6.1 years ago skkujin • 0
0
votes
5
replies
1.9k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Is C adjusted for purity?
PureCN Adjusted C
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
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9
replies
1.8k
views
Unable to find solution: low coverage
PureCN fatal error no solution
6.2 years ago twtoal ▴ 10
0
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2
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926
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 6.2 years ago by ▴ 130 • written 6.2 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
6.2 years ago twtoal ▴ 10
0
votes
6
replies
1.4k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
6.2 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
1.3k
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
990
views
Dx.R somatic_ontarget column
PureCN
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
votes
1
reply
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
1.0k
views
PureCN Release Notes
PureCN Release
updated 6.2 years ago by 66k • written 6.2 years ago by ▴ 10
0
votes
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 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
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4
replies
1.4k
views
PureCN error: zero-length 'labels' specified
PureCN
6.3 years ago twtoal ▴ 10
0
votes
1
reply
842
views
PureCN Panel of Normals contents
PureCN
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
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2
replies
1.0k
views
No CNAs or SNVs in results
PureCN
6.3 years ago twtoal ▴ 10
3
votes
5
replies
1.7k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 6.2 years ago by • 0 • written 6.3 years ago by ▴ 10
1
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1
reply
1.0k
views
PureCN support for indels
PureCN indels
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
votes
9
replies
1.5k
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
votes
3
replies
1.3k
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
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Scholar to Michael Love 42k
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Scholar to Gordon Smyth 51k
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