Showing : PureCN • reset
0
votes
0
replies
785
views
Calculating tumour purity having only CNA data
PureCN CNA purity cancer
2.0 years ago JAcky • 0
1
vote
5
replies
1.7k
views
Mutect version, matched normal and manual curation in PureCN
PureCN
2.1 years ago • updated 17 months ago Ken C • 0
1
vote
8
replies
1.6k
views
PureCN: Copy Number of 7 issue
Pure PureCN
updated 2.6 years ago by ▴ 130 • written 2.6 years ago by • 0
1
vote
5
replies
1.4k
views
PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 2.6 years ago by ▴ 130 • written 2.6 years ago by ▴ 10
0
votes
2
replies
1.0k
views
PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 2.8 years ago by ▴ 130 • written 2.8 years ago by ▴ 10
0
votes
1
reply
764
views
PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 2.9 years ago by ▴ 130 • written 2.9 years ago by ▴ 10
0
votes
3
replies
919
views
Corrupt data in Sex column of .csv file
PureCN
3.2 years ago twtoal ▴ 10
0
votes
2
replies
1.3k
views
PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
4.0 years ago twtoal ▴ 10
0
votes
3
replies
1.1k
views
PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 4.1 years ago by ▴ 130 • written 4.1 years ago by ▴ 10
0
votes
4
replies
1.0k
views
Why is PureCN LOH file missing some segments
purecn loh
4.3 years ago twtoal ▴ 10
0
votes
1
reply
835
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 4.5 years ago by ▴ 130 • written 4.5 years ago by • 0
0
votes
2
replies
1.2k
views
PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 4.6 years ago by ★ 6.5k • written 4.6 years ago by ▴ 10
0
votes
3
replies
952
views
callLOH output file NA values
PureCN NA values
updated 5.2 years ago by ▴ 130 • written 5.2 years ago by ▴ 10
0
votes
1
reply
1.1k
views
PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 5.2 years ago by ▴ 130 • written 5.2 years ago by ▴ 10
0
votes
1
reply
912
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
5.6 years ago twtoal ▴ 10
2
votes
5
replies
2.7k
views
Issue with BiocParallel
purecn biocparallel
5.7 years ago milos-91 • 0
0
votes
1
reply
910
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
votes
3
replies
1.2k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
5.7 years ago twtoal ▴ 10
0
votes
1
reply
1.1k
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
votes
2
replies
941
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
5.8 years ago • updated 5.7 years ago twtoal ▴ 10
0
votes
1
reply
1.1k
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
5.8 years ago twtoal ▴ 10
0
votes
2
replies
1.2k
views
CNV in Normal Samples?
PureCN Germline Normal CNV
updated 5.8 years ago by ▴ 130 • written 5.8 years ago by ▴ 10
1
vote
1
reply
916
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
votes
1
reply
787
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
1
vote
3
replies
1.1k
views
PureCN Manual Curation .rds file
PureCN rds_file manual_curation
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
votes
4
replies
1.4k
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
votes
3
replies
1.9k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
6.0 years ago • updated 5.9 years ago twtoal ▴ 10
0
votes
1
reply
1.2k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
6.0 years ago twtoal ▴ 10
0
votes
6
replies
1.7k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
6.1 years ago skkujin • 0
0
votes
5
replies
1.9k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
3
votes
5
replies
1.7k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 6.1 years ago by • 0 • written 6.2 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Is C adjusted for purity?
PureCN Adjusted C
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
0
votes
9
replies
1.8k
views
Unable to find solution: low coverage
PureCN fatal error no solution
6.1 years ago twtoal ▴ 10
0
votes
2
replies
904
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
0
votes
4
replies
1.3k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
6.1 years ago twtoal ▴ 10
0
votes
6
replies
1.3k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
6.1 years ago twtoal ▴ 10
0
votes
2
replies
1.4k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
votes
4
replies
1.2k
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN Somatic Mutations
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
votes
2
replies
966
views
Dx.R somatic_ontarget column
PureCN
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
votes
1
reply
1.0k
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
1
vote
3
replies
997
views
PureCN Release Notes
PureCN Release
updated 6.2 years ago by 66k • written 6.2 years ago by ▴ 10
0
votes
1
reply
1.9k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
votes
3
replies
1.0k
views
PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
votes
4
replies
1.4k
views
PureCN error: zero-length 'labels' specified
PureCN
6.2 years ago twtoal ▴ 10
0
votes
1
reply
823
views
PureCN Panel of Normals contents
PureCN
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
votes
2
replies
1.0k
views
No CNAs or SNVs in results
PureCN
6.2 years ago twtoal ▴ 10
1
vote
1
reply
998
views
PureCN support for indels
PureCN indels
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
0
votes
9
replies
1.4k
views
errors in version 1.7.53
PureCN
updated 6.8 years ago by ▴ 130 • written 6.8 years ago by • 0
0
votes
1
reply
1.1k
views
errors in Purecn callLOH
PureCN
updated 6.8 years ago by ▴ 130 • written 6.8 years ago by • 0
2
votes
3
replies
1.2k
views
PureCN can classify indel variants as germline vs. somatic ?
PureCN indel somatic germline
updated 7.1 years ago by ▴ 130 • written 7.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ranking the GSEA Results by Lluís Revilla Sancho ▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction by Antonio • 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results by alserg ▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results by alserg ▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Votes
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
Awards • All
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to ATpoint ★ 4.2k
Popular Question to WouterDeCoster ▴ 130
Scholar to Gordon Smyth 51k
Voter to Chris ▴ 20
Locations • All
United States, 1 minute ago
St Louis, MO, 10 minutes ago
European Union, 10 minutes ago
Switzerland, 13 minutes ago
Germany, 13 minutes ago
Traffic: 1304 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6