Showing : Purecn • reset
0
votes
0
replies
732
views
Calculating tumour purity having only CNA data
PureCN CNA purity cancer
22 months ago JAcky • 0
1
vote
5
replies
1.5k
views
Mutect version, matched normal and manual curation in PureCN
PureCN
22 months ago • updated 15 months ago Ken C • 0
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
1
vote
5
replies
1.3k
views
PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 2.4 years ago by ▴ 130 • written 2.5 years ago by ▴ 10
0
votes
2
replies
981
views
PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 2.6 years ago by ▴ 130 • written 2.6 years ago by ▴ 10
0
votes
1
reply
694
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
3
replies
864
views
Corrupt data in Sex column of .csv file
PureCN
3.0 years ago twtoal ▴ 10
0
votes
2
replies
1.1k
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
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
4
replies
968
views
Why is PureCN LOH file missing some segments
purecn loh
4.1 years ago twtoal ▴ 10
0
votes
1
reply
793
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
2
replies
1.1k
views
PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 4.4 years ago by ★ 6.5k • written 4.4 years ago by ▴ 10
0
votes
3
replies
902
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
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
874
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
5.4 years ago twtoal ▴ 10
2
votes
5
replies
2.5k
views
Issue with BiocParallel
purecn biocparallel
5.5 years ago milos-91 • 0
0
votes
1
reply
872
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 5.5 years ago by ▴ 130 • written 5.5 years ago by ▴ 10
0
votes
3
replies
1.1k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
5.5 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
2
replies
899
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
5.6 years ago twtoal ▴ 10
0
votes
1
reply
1.0k
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
5.6 years ago twtoal ▴ 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
1
vote
1
reply
865
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
votes
1
reply
745
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 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
4
replies
1.3k
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
3
replies
1.8k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
5.8 years ago • updated 5.7 years ago twtoal ▴ 10
0
votes
1
reply
1.2k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
5.8 years ago twtoal ▴ 10
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
5
replies
1.8k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
3
votes
5
replies
1.6k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 5.9 years ago by • 0 • written 6.1 years ago by ▴ 10
0
votes
1
reply
959
views
Is C adjusted for purity?
PureCN Adjusted C
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
votes
9
replies
1.6k
views
Unable to find solution: low coverage
PureCN fatal error no solution
5.9 years ago twtoal ▴ 10
0
votes
2
replies
869
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
votes
4
replies
1.2k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
5.9 years ago twtoal ▴ 10
0
votes
6
replies
1.3k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
6.0 years ago twtoal ▴ 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
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
votes
2
replies
908
views
Dx.R somatic_ontarget column
PureCN
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
1
reply
982
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
1
vote
3
replies
946
views
PureCN Release Notes
PureCN Release
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 10
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
3
replies
972
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
0
votes
4
replies
1.3k
views
PureCN error: zero-length 'labels' specified
PureCN
6.0 years ago twtoal ▴ 10
0
votes
1
reply
780
views
PureCN Panel of Normals contents
PureCN
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
2
replies
978
views
No CNAs or SNVs in results
PureCN
6.0 years ago twtoal ▴ 10
1
vote
1
reply
943
views
PureCN support for indels
PureCN indels
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
0
votes
9
replies
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
1
reply
1.1k
views
errors in Purecn callLOH
PureCN
updated 6.6 years ago by ▴ 130 • written 6.6 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 6.9 years ago by ▴ 130 • written 6.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 30
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Awards • All
Popular Question to Leo Lahti ▴ 30
Scholar to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Scholar to Michael Love 41k
Supporter to JKim • 0
Locations • All
Melbourne, Australia, 10 minutes ago
France, 12 minutes ago
WEHI, Melbourne, Australia, 26 minutes ago
Finland, 1 hour ago
Canada, 1 hour ago
Traffic: 769 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