Showing : purecn • reset
1
vote
5
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698
views
Mutect version, matched normal and manual curation in PureCN
PureCN
11 months ago • updated 4 months ago Ken C • 0
0
votes
0
replies
354
views
Calculating tumour purity having only CNA data
PureCN CNA purity cancer
11 months ago JAcky • 0
1
vote
8
replies
954
views
PureCN: Copy Number of 7 issue
Pure PureCN
updated 18 months ago by ▴ 130 • written 18 months ago by • 0
1
vote
5
replies
863
views
PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 18 months ago by ▴ 130 • written 19 months ago by ▴ 10
0
votes
2
replies
646
views
PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 21 months ago by ▴ 130 • written 21 months ago by ▴ 10
0
votes
1
reply
439
views
PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 22 months ago by ▴ 130 • written 22 months ago by ▴ 10
0
votes
3
replies
564
views
Corrupt data in Sex column of .csv file
PureCN
2.1 years ago twtoal ▴ 10
0
votes
2
replies
760
views
PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
3.0 years ago twtoal ▴ 10
0
votes
3
replies
640
views
PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 3.1 years ago by ▴ 130 • written 3.1 years ago by ▴ 10
0
votes
4
replies
621
views
Why is PureCN LOH file missing some segments
purecn loh
3.3 years ago twtoal ▴ 10
0
votes
1
reply
477
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 3.5 years ago by ▴ 130 • written 3.5 years ago by • 0
0
votes
2
replies
824
views
PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 3.5 years ago by ★ 6.0k • written 3.5 years ago by ▴ 10
0
votes
3
replies
610
views
callLOH output file NA values
PureCN NA values
updated 4.1 years ago by ▴ 130 • written 4.1 years ago by ▴ 10
0
votes
1
reply
620
views
PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 4.1 years ago by ▴ 130 • written 4.1 years ago by ▴ 10
0
votes
1
reply
656
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
4.5 years ago twtoal ▴ 10
2
votes
5
replies
1.9k
views
Issue with BiocParallel
purecn biocparallel
4.6 years ago milos-91 • 0
0
votes
1
reply
604
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 4.6 years ago by ▴ 130 • written 4.6 years ago by ▴ 10
0
votes
3
replies
729
views
Assigning DUP/DEL p-value to CNV segment
PureCN
4.7 years ago twtoal ▴ 10
0
votes
1
reply
748
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 4.7 years ago by ▴ 130 • written 4.7 years ago by ▴ 10
0
votes
2
replies
618
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
4.7 years ago twtoal ▴ 10
0
votes
1
reply
670
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
4.7 years ago twtoal ▴ 10
0
votes
2
replies
777
views
CNV in Normal Samples?
PureCN Germline Normal CNV
updated 4.7 years ago by ▴ 130 • written 4.7 years ago by ▴ 10
1
vote
1
reply
640
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 4.8 years ago by ▴ 130 • written 4.8 years ago by ▴ 10
0
votes
1
reply
508
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 4.8 years ago by ▴ 130 • written 4.8 years ago by ▴ 10
1
vote
3
replies
705
views
PureCN Manual Curation .rds file
PureCN rds_file manual_curation
updated 4.8 years ago by ▴ 130 • written 4.8 years ago by ▴ 10
0
votes
4
replies
993
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 4.8 years ago by ▴ 130 • written 4.8 years ago by ▴ 10
0
votes
3
replies
1.5k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
5.0 years ago • updated 4.8 years ago twtoal ▴ 10
0
votes
1
reply
848
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
5.0 years ago twtoal ▴ 10
0
votes
6
replies
1.2k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
5.0 years ago skkujin • 0
0
votes
5
replies
1.3k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 5.0 years ago by ▴ 130 • written 5.0 years ago by ▴ 10
3
votes
5
replies
1.2k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 5.0 years ago by • 0 • written 5.2 years ago by ▴ 10
0
votes
1
reply
639
views
Is C adjusted for purity?
PureCN Adjusted C
updated 5.0 years ago by ▴ 130 • written 5.0 years ago by ▴ 10
0
votes
9
replies
1.1k
views
Unable to find solution: low coverage
PureCN fatal error no solution
5.0 years ago twtoal ▴ 10
0
votes
2
replies
634
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 5.0 years ago by ▴ 130 • written 5.0 years ago by ▴ 10
0
votes
4
replies
867
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
5.0 years ago twtoal ▴ 10
0
votes
6
replies
883
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
5.1 years ago twtoal ▴ 10
0
votes
2
replies
886
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 5.1 years ago by ▴ 130 • written 5.1 years ago by ▴ 10
0
votes
4
replies
746
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN Somatic Mutations
updated 5.1 years ago by ▴ 130 • written 5.1 years ago by ▴ 10
0
votes
2
replies
608
views
Dx.R somatic_ontarget column
PureCN
updated 5.1 years ago by ▴ 130 • written 5.1 years ago by ▴ 10
0
votes
1
reply
722
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 5.1 years ago by ▴ 130 • written 5.1 years ago by ▴ 10
1
vote
3
replies
676
views
PureCN Release Notes
PureCN Release
updated 5.1 years ago by 63k • written 5.1 years ago by ▴ 10
0
votes
1
reply
1.5k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 5.1 years ago by ▴ 130 • written 5.1 years ago by ▴ 10
0
votes
3
replies
682
views
PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 5.1 years ago by ▴ 130 • written 5.1 years ago by ▴ 10
0
votes
4
replies
943
views
PureCN error: zero-length 'labels' specified
PureCN
5.1 years ago twtoal ▴ 10
0
votes
1
reply
517
views
PureCN Panel of Normals contents
PureCN
updated 5.1 years ago by ▴ 130 • written 5.1 years ago by ▴ 10
0
votes
2
replies
681
views
No CNAs or SNVs in results
PureCN
5.1 years ago twtoal ▴ 10
1
vote
1
reply
655
views
PureCN support for indels
PureCN indels
updated 5.2 years ago by ▴ 130 • written 5.2 years ago by ▴ 10
0
votes
9
replies
873
views
errors in version 1.7.53
PureCN
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by • 0
0
votes
1
reply
785
views
errors in Purecn callLOH
PureCN
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by • 0
2
votes
3
replies
892
views
PureCN can classify indel variants as germline vs. somatic ?
PureCN indel somatic germline
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by • 0
50 results • Page 1 of 1
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Comment: Handling NA's in Deseq2 by Asger Mølgaard • 0
Dear ATpoint Thank you for your response - it works like a charm! You just saved a PhD-study! Thank you :)
Comment: Ensembl plants at annotationHub? by Bruno • 0
Hi Guido, Thanks for your fast reply the error was as said in my question "Annotation must be a GRanges object", when I tried to use the a…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 3.6k
You did not show the code that resulted in that error, so we have to guess what you did. Yet, the [R package][1] `Signac` contains the func…
Comment: Query regarding phyloseq object construct with QIIME output by betterwound • 0
Thanks for sharing the code [geometry dash](https://geometrydash.io/)
Answer: Ensembl plants at annotationHub? by Bruno • 0
Hi Johannes, First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant commu…
Votes
C: Minimum number of samples per treatment/group for WGCNA analysis
A: Minimum number of samples per treatment/group for WGCNA analysis
Minimum number of samples per treatment/group for WGCNA analysis
Comment: DESeq2 on multilevel design variable
Comment: Ensembl plants at annotationHub?
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