Showing : PureCN • reset
0
votes
9
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1.4k
views
errors in version 1.7.53
PureCN
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by • 0
0
votes
9
replies
1.7k
views
Unable to find solution: low coverage
PureCN fatal error no solution
6.0 years ago twtoal ▴ 10
1
vote
8
replies
1.5k
views
PureCN: Copy Number of 7 issue
Pure PureCN
updated 2.4 years ago by ▴ 130 • written 2.4 years ago by • 0
0
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8
replies
1.5k
views
Error in running development version of PureCN
PureCN software error
7.6 years ago hustlxc • 0
0
votes
6
replies
1.7k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
5.9 years ago skkujin • 0
0
votes
6
replies
1.3k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
6.0 years ago twtoal ▴ 10
1
vote
5
replies
1.5k
views
Mutect version, matched normal and manual curation in PureCN
PureCN
23 months ago • updated 15 months ago Ken C • 0
3
votes
5
replies
1.6k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 6.0 years ago by • 0 • written 6.1 years ago by ▴ 10
0
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5
replies
1.8k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
2
votes
5
replies
2.6k
views
Issue with BiocParallel
purecn biocparallel
5.5 years ago milos-91 • 0
1
vote
5
replies
1.3k
views
PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 2.5 years ago by ▴ 130 • written 2.5 years ago by ▴ 10
0
votes
4
replies
1.3k
views
PureCN error: zero-length 'labels' specified
PureCN
6.0 years ago twtoal ▴ 10
0
votes
4
replies
1.2k
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN Somatic Mutations
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
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4
replies
1.4k
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
votes
4
replies
979
views
Why is PureCN LOH file missing some segments
purecn loh
4.2 years ago twtoal ▴ 10
0
votes
4
replies
1.2k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
6.0 years ago twtoal ▴ 10
1
vote
3
replies
958
views
PureCN Release Notes
PureCN Release
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 10
0
votes
3
replies
1.0k
views
PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 4.0 years ago by ▴ 130 • written 4.0 years ago by ▴ 10
0
votes
3
replies
1.9k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
5.9 years ago • updated 5.7 years ago twtoal ▴ 10
0
votes
3
replies
982
views
PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
2
votes
3
replies
1.2k
views
PureCN can classify indel variants as germline vs. somatic ?
PureCN indel somatic germline
updated 6.9 years ago by ▴ 130 • written 6.9 years ago by • 0
0
votes
3
replies
917
views
callLOH output file NA values
PureCN NA values
updated 5.0 years ago by ▴ 130 • written 5.0 years ago by ▴ 10
0
votes
3
replies
875
views
Corrupt data in Sex column of .csv file
PureCN
3.0 years ago twtoal ▴ 10
1
vote
3
replies
1.0k
views
PureCN Manual Curation .rds file
PureCN rds_file manual_curation
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
votes
3
replies
1.1k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
5.6 years ago twtoal ▴ 10
0
votes
2
replies
876
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
2
replies
984
views
No CNAs or SNVs in results
PureCN
6.0 years ago twtoal ▴ 10
0
votes
2
replies
922
views
Dx.R somatic_ontarget column
PureCN
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
2
replies
1.3k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
2
replies
1.1k
views
CNV in Normal Samples?
PureCN Germline Normal CNV
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
votes
2
replies
910
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
5.6 years ago twtoal ▴ 10
0
votes
2
replies
1.1k
views
PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 4.5 years ago by ★ 6.5k • written 4.5 years ago by ▴ 10
0
votes
2
replies
1.2k
views
PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
3.9 years ago twtoal ▴ 10
0
votes
2
replies
994
views
PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 2.7 years ago by ▴ 130 • written 2.7 years ago by ▴ 10
0
votes
1
reply
1.0k
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
5.6 years ago twtoal ▴ 10
0
votes
1
reply
1.0k
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
votes
1
reply
974
views
Is C adjusted for purity?
PureCN Adjusted C
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
1
reply
880
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
1
vote
1
reply
947
views
Bug Report/Question for PureCN: createSNPBlacklist() Error
PureCN
updated 7.9 years ago by ▴ 130 • written 7.9 years ago by ▴ 10
0
votes
1
reply
881
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
5.4 years ago twtoal ▴ 10
0
votes
1
reply
1.0k
views
PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 5.0 years ago by ▴ 130 • written 5.0 years ago by ▴ 10
0
votes
1
reply
993
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
1
reply
688
views
Error in running example code of PureCN
PureCN
updated 7.6 years ago by ▴ 130 • written 7.6 years ago by • 0
0
votes
1
reply
804
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 4.4 years ago by ▴ 130 • written 4.4 years ago by • 0
0
votes
1
reply
1.8k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
1
reply
795
views
PureCN Panel of Normals contents
PureCN
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
1
reply
966
views
how to make sure PureCN gets somatic status from VCF?
PureCN
updated 7.4 years ago by ▴ 130 • written 7.4 years ago by • 0
1
vote
1
reply
954
views
PureCN support for indels
PureCN indels
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
0
votes
1
reply
709
views
PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 2.7 years ago by ▴ 130 • written 2.7 years ago by ▴ 10
0
votes
1
reply
1.2k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
5.9 years ago twtoal ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Awards • All
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Popular Question to ATpoint ★ 4.1k
Teacher to Michael Love 42k
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