Showing : PureCN • reset
1
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4
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BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN biomaRt
updated 4 weeks ago by • 0 • written 3 months ago by • 0
0
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0
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946
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Calculating tumour purity having only CNA data
PureCN CNA purity cancer
2.4 years ago JAcky • 0
1
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5
replies
2.0k
views
Mutect version, matched normal and manual curation in PureCN
PureCN
2.5 years ago • updated 22 months ago Ken C • 0
1
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8
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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
1
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5
replies
1.7k
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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
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2
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1.2k
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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
896
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PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 3.3 years ago by ▴ 130 • written 3.3 years ago by ▴ 10
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3
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1.1k
views
Corrupt data in Sex column of .csv file
PureCN
3.6 years ago twtoal ▴ 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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3
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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
0
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4
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1.2k
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Why is PureCN LOH file missing some segments
purecn loh
4.8 years ago twtoal ▴ 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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2
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1.4k
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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
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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
1.3k
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
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1
reply
1.0k
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
6.0 years ago twtoal ▴ 10
2
votes
5
replies
2.9k
views
Issue with BiocParallel
purecn biocparallel
6.1 years ago milos-91 • 0
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
0
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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
1.2k
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
0
votes
2
replies
1.1k
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
6.2 years ago twtoal ▴ 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
votes
2
replies
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
1
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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
908
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
1
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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
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
votes
3
replies
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
votes
1
reply
1.4k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
6.5 years ago twtoal ▴ 10
0
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6
replies
2.0k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
6.5 years ago skkujin • 0
0
votes
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
votes
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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9
replies
2.1k
views
Unable to find solution: low coverage
PureCN fatal error no solution
6.6 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
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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
votes
6
replies
1.5k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
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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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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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
0
votes
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
1
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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
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
0
votes
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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4
replies
1.6k
views
PureCN error: zero-length 'labels' specified
PureCN
6.6 years ago twtoal ▴ 10
0
votes
1
reply
930
views
PureCN Panel of Normals contents
PureCN
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
votes
2
replies
1.1k
views
No CNAs or SNVs in results
PureCN
6.6 years ago twtoal ▴ 10
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
vote
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
votes
9
replies
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
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
50 results • Page 1 of 1
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Replies
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.
Comment: RSubread output significantly different from bash Subread output by Aimee • 0
Hi Gordon, Thank you so much for this response. I went back and checked, and you are absolutely correct that it was shown in the settings b…
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
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