Showing : PureCN • reset
2
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5
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2.9k
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Issue with BiocParallel
purecn biocparallel
6.1 years ago milos-91 • 0
0
votes
3
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2.1k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
6.5 years ago • updated 6.3 years ago twtoal ▴ 10
0
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5
replies
2.1k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 6.5 years ago by ▴ 130 • written 6.5 years ago by ▴ 10
0
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9
replies
2.1k
views
Unable to find solution: low coverage
PureCN fatal error no solution
6.6 years ago twtoal ▴ 10
0
votes
1
reply
2.0k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
1
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5
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2.0k
views
Mutect version, matched normal and manual curation in PureCN
PureCN
2.5 years ago • updated 22 months ago Ken C • 0
0
votes
6
replies
2.0k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
6.5 years ago skkujin • 0
3
votes
5
replies
1.9k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 6.5 years ago by • 0 • written 6.7 years ago by ▴ 10
1
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8
replies
1.9k
views
PureCN: Copy Number of 7 issue
Pure PureCN
updated 3.0 years ago by ▴ 130 • written 3.0 years ago by • 0
0
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8
replies
1.8k
views
Error in running development version of PureCN
PureCN software error
8.2 years ago hustlxc • 0
1
vote
5
replies
1.7k
views
PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 3.1 years ago by ▴ 130 • written 3.1 years ago by ▴ 10
0
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9
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1.7k
views
errors in version 1.7.53
PureCN
updated 7.2 years ago by ▴ 130 • written 7.2 years ago by • 0
0
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4
replies
1.6k
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
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4
replies
1.6k
views
PureCN error: zero-length 'labels' specified
PureCN
6.6 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 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 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
4.5 years ago twtoal ▴ 10
0
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6
replies
1.5k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
6.6 years ago twtoal ▴ 10
0
votes
4
replies
1.4k
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN Somatic Mutations
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
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4
replies
1.4k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
6.6 years ago twtoal ▴ 10
0
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1
reply
1.4k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
6.5 years ago twtoal ▴ 10
0
votes
3
replies
1.4k
views
PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 4.6 years ago by ▴ 130 • written 4.6 years ago by ▴ 10
2
votes
3
replies
1.4k
views
PureCN can classify indel variants as germline vs. somatic ?
PureCN indel somatic germline
updated 7.5 years ago by ▴ 130 • written 7.5 years ago by • 0
0
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2
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1.4k
views
CNV in Normal Samples?
PureCN Germline Normal CNV
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
votes
2
replies
1.4k
views
PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 5.0 years ago by ★ 6.6k • written 5.0 years ago by ▴ 10
0
votes
3
replies
1.3k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
6.2 years ago twtoal ▴ 10
0
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1
reply
1.3k
views
PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
1
vote
3
replies
1.3k
views
PureCN Manual Curation .rds file
PureCN rds_file manual_curation
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
votes
1
reply
1.2k
views
errors in Purecn callLOH
PureCN
updated 7.2 years ago by ▴ 130 • written 7.2 years ago by • 0
0
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2
replies
1.2k
views
PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 3.2 years ago by ▴ 130 • written 3.3 years ago by ▴ 10
0
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1
reply
1.2k
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
6.2 years ago twtoal ▴ 10
0
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4
replies
1.2k
views
Why is PureCN LOH file missing some segments
purecn loh
4.8 years ago twtoal ▴ 10
0
votes
1
reply
1.2k
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
1
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1
reply
1.2k
views
PureCN support for indels
PureCN indels
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
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3
replies
1.2k
views
PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
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1
reply
1.2k
views
Is C adjusted for purity?
PureCN Adjusted C
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
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2
replies
1.1k
views
No CNAs or SNVs in results
PureCN
6.6 years ago twtoal ▴ 10
1
vote
3
replies
1.1k
views
PureCN Release Notes
PureCN Release
updated 6.6 years ago by 67k • written 6.6 years ago by ▴ 10
0
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1
reply
1.1k
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
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3
replies
1.1k
views
callLOH output file NA values
PureCN NA values
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
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1
reply
1.1k
views
how to make sure PureCN gets somatic status from VCF?
PureCN
updated 8.0 years ago by ▴ 130 • written 8.0 years ago by • 0
0
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2
replies
1.1k
views
Dx.R somatic_ontarget column
PureCN
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
1
vote
1
reply
1.1k
views
Bug Report/Question for PureCN: createSNPBlacklist() Error
PureCN
updated 8.4 years ago by ▴ 130 • written 8.4 years ago by ▴ 10
0
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2
replies
1.1k
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
6.2 years ago twtoal ▴ 10
0
votes
3
replies
1.1k
views
Corrupt data in Sex column of .csv file
PureCN
3.6 years ago twtoal ▴ 10
0
votes
1
reply
1.0k
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 6.1 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
1
vote
1
reply
1.0k
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
6.0 years ago twtoal ▴ 10
0
votes
2
replies
1.0k
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
votes
1
reply
967
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 5.0 years ago by ▴ 130 • written 5.0 years ago by • 0
0
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0
replies
946
views
Calculating tumour purity having only CNA data
PureCN CNA purity cancer
2.4 years ago JAcky • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Advice needed: Using limma for differential pathway analysis with continuous dis by Gordon Smyth 52k
limma has always handled any combination of continuous or categorical variables from the very beginning. You simply add continuous variable…
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi @yangliao, thanks for the note. We use Feature Counts extensively for gene-level counting (exon features). Unfortunately though, and I…
Comment: Feature Counts - potential bug with outfile.jcounts by Yang Liao ▴ 450
When you use `featureCounts` to count junctions with the `-J` option, it doesn't check if the junction is exactly overlap with exons of gen…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe by ATpoint ★ 4.6k
I think you run into the common pitfall that you treat results as categorical (significant, not significant) whereas in reality the results…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe by swbarnes2 ★ 1.4k
It would probably help if you broke out the raw and normalized read counts for all the samples.
Votes
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: Running multiple KNN queries in parallel
Awards • All
Popular Question to Tadeoye ▴ 20
Teacher to Gordon Smyth 52k
Scholar to Aaron Lun ★ 28k
Teacher to Michael Love 43k
Popular Question to Dario Strbenac ★ 1.5k
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