Showing : Purecn • reset
1
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4
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937
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BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN biomaRt
updated 10 weeks ago by • 0 • written 4 months ago by • 0
0
votes
0
replies
962
views
Calculating tumour purity having only CNA data
PureCN CNA purity cancer
2.6 years ago JAcky • 0
1
vote
5
replies
2.1k
views
Mutect version, matched normal and manual curation in PureCN
PureCN
2.6 years ago • updated 23 months ago Ken C • 0
1
vote
8
replies
1.9k
views
PureCN: Copy Number of 7 issue
Pure PureCN
updated 3.1 years ago by ▴ 130 • written 3.1 years ago by • 0
1
vote
5
replies
1.8k
views
PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 3.2 years ago by ▴ 130 • written 3.2 years ago by ▴ 10
0
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2
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1.3k
views
PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 3.4 years ago by ▴ 130 • written 3.4 years ago by ▴ 10
0
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1
reply
915
views
PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 3.4 years ago by ▴ 130 • written 3.4 years ago by ▴ 10
0
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3
replies
1.1k
views
Corrupt data in Sex column of .csv file
PureCN
3.7 years ago twtoal ▴ 10
0
votes
2
replies
1.6k
views
PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
4.6 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 4.7 years ago by ▴ 130 • written 4.7 years ago by ▴ 10
0
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4
replies
1.2k
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Why is PureCN LOH file missing some segments
purecn loh
4.9 years ago twtoal ▴ 10
0
votes
1
reply
988
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 5.1 years ago by ▴ 130 • written 5.1 years ago by • 0
0
votes
2
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1.4k
views
PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 5.2 years ago by ★ 6.6k • written 5.2 years ago by ▴ 10
0
votes
3
replies
1.2k
views
callLOH output file NA values
PureCN NA values
updated 5.7 years ago by ▴ 130 • written 5.7 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 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
6.1 years ago twtoal ▴ 10
2
votes
5
replies
3.0k
views
Issue with BiocParallel
purecn biocparallel
6.2 years ago milos-91 • 0
0
votes
1
reply
1.1k
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
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3
replies
1.4k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
6.3 years ago twtoal ▴ 10
0
votes
1
reply
1.2k
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
6.3 years ago twtoal ▴ 10
0
votes
1
reply
1.2k
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
6.3 years ago twtoal ▴ 10
0
votes
2
replies
1.4k
views
CNV in Normal Samples?
PureCN Germline Normal CNV
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
1
vote
1
reply
1.0k
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 6.4 years ago by ▴ 130 • written 6.4 years ago by ▴ 10
0
votes
1
reply
928
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 6.4 years ago by ▴ 130 • written 6.4 years ago by ▴ 10
1
vote
3
replies
1.3k
views
PureCN Manual Curation .rds file
PureCN rds_file manual_curation
updated 6.4 years ago by ▴ 130 • written 6.4 years ago by ▴ 10
0
votes
4
replies
1.7k
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 6.4 years ago by ▴ 130 • written 6.4 years ago by ▴ 10
0
votes
3
replies
2.1k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
6.6 years ago • updated 6.4 years ago twtoal ▴ 10
0
votes
1
reply
1.4k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
6.6 years ago twtoal ▴ 10
0
votes
6
replies
2.0k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
6.6 years ago skkujin • 0
0
votes
5
replies
2.1k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
3
votes
5
replies
1.9k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 6.6 years ago by • 0 • written 6.8 years ago by ▴ 10
0
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1
reply
1.2k
views
Is C adjusted for purity?
PureCN Adjusted C
updated 6.7 years ago by ▴ 130 • written 6.7 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
6.7 years ago twtoal ▴ 10
0
votes
2
replies
1.0k
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
votes
4
replies
1.5k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
6.7 years ago twtoal ▴ 10
0
votes
6
replies
1.6k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
6.7 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 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
votes
4
replies
1.5k
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN Somatic Mutations
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Dx.R somatic_ontarget column
PureCN
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
votes
1
reply
1.2k
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
1
vote
3
replies
1.2k
views
PureCN Release Notes
PureCN Release
updated 6.7 years ago by 67k • written 6.7 years ago by ▴ 10
0
votes
1
reply
2.1k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
votes
3
replies
1.2k
views
PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
votes
4
replies
1.6k
views
PureCN error: zero-length 'labels' specified
PureCN
6.7 years ago twtoal ▴ 10
0
votes
1
reply
952
views
PureCN Panel of Normals contents
PureCN
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
votes
2
replies
1.2k
views
No CNAs or SNVs in results
PureCN
6.7 years ago twtoal ▴ 10
1
vote
1
reply
1.2k
views
PureCN support for indels
PureCN indels
updated 6.8 years ago by ▴ 130 • written 6.8 years ago by ▴ 10
0
votes
9
replies
1.7k
views
errors in version 1.7.53
PureCN
updated 7.3 years ago by ▴ 130 • written 7.3 years ago by • 0
0
votes
1
reply
1.3k
views
errors in Purecn callLOH
PureCN
updated 7.3 years ago by ▴ 130 • written 7.3 years ago by • 0
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Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
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