Showing : Purecn • reset
0
votes
8
replies
1.5k
views
Error in running development version of PureCN
PureCN software error
7.6 years ago • updated 7.5 years ago hustlxc • 0
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
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
4
replies
1.3k
views
PureCN error: zero-length 'labels' specified
PureCN
6.0 years ago twtoal ▴ 10
0
votes
2
replies
905
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
5.6 years ago twtoal ▴ 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
1
vote
1
reply
951
views
PureCN support for indels
PureCN indels
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
0
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2
replies
983
views
No CNAs or SNVs in results
PureCN
6.0 years ago twtoal ▴ 10
0
votes
1
reply
791
views
PureCN Panel of Normals contents
PureCN
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
1
vote
1
reply
937
views
Bug Report/Question for PureCN: createSNPBlacklist() Error
PureCN
updated 7.8 years ago by ▴ 130 • written 7.8 years ago by ▴ 10
0
votes
3
replies
979
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
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
1
vote
3
replies
951
views
PureCN Release Notes
PureCN Release
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 10
0
votes
1
reply
989
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
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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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
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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
875
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
1
reply
970
views
Is C adjusted for purity?
PureCN Adjusted C
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
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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
0
votes
2
replies
918
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
686
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
962
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
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
1
reply
1.1k
views
errors in Purecn callLOH
PureCN
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by • 0
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
3
replies
913
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
801
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
4
replies
977
views
Why is PureCN LOH file missing some segments
purecn loh
4.2 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
1
reply
703
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
871
views
Corrupt data in Sex column of .csv file
PureCN
3.0 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
votes
2
replies
989
views
PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 2.6 years ago by ▴ 130 • written 2.7 years ago by ▴ 10
0
votes
3
replies
1.8k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
5.9 years ago • updated 5.7 years ago twtoal ▴ 10
0
votes
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
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
1
reply
749
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
1
reply
869
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 5.7 years ago by ▴ 130 • written 5.7 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
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
3
replies
1.1k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
5.6 years ago twtoal ▴ 10
0
votes
1
reply
878
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 5.5 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
votes
1
reply
879
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
5.4 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
1
reply
1.2k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
5.9 years ago twtoal ▴ 10
0
votes
9
replies
1.7k
views
Unable to find solution: low coverage
PureCN fatal error no solution
6.0 years ago twtoal ▴ 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
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
50 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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