Showing : purecn • reset
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BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN biomaRt
updated 14 days ago by • 0 • written 12 weeks ago by • 0
0
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0
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933
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Calculating tumour purity having only CNA data
PureCN CNA purity cancer
2.4 years ago JAcky • 0
1
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5
replies
2.0k
views
Mutect version, matched normal and manual curation in PureCN
PureCN
2.4 years ago • updated 21 months ago Ken C • 0
1
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8
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1.9k
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PureCN: Copy Number of 7 issue
Pure PureCN
updated 3.0 years ago by ▴ 130 • written 3.0 years ago by • 0
1
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5
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1.7k
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PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 3.0 years ago by ▴ 130 • written 3.0 years ago by ▴ 10
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2
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1.2k
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PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 3.2 years ago by ▴ 130 • written 3.2 years ago by ▴ 10
0
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1
reply
889
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PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 3.3 years ago by ▴ 130 • written 3.3 years ago by ▴ 10
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3
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1.1k
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Corrupt data in Sex column of .csv file
PureCN
3.6 years ago twtoal ▴ 10
0
votes
2
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1.5k
views
PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
4.4 years ago twtoal ▴ 10
0
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3
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1.4k
views
PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 4.5 years ago by ▴ 130 • written 4.5 years ago by ▴ 10
0
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4
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1.2k
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Why is PureCN LOH file missing some segments
purecn loh
4.7 years ago twtoal ▴ 10
0
votes
1
reply
955
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 4.9 years ago by ▴ 130 • written 4.9 years ago by • 0
0
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2
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1.4k
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PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 5.0 years ago by ★ 6.6k • written 5.0 years ago by ▴ 10
0
votes
3
replies
1.1k
views
callLOH output file NA values
PureCN NA values
updated 5.5 years ago by ▴ 130 • written 5.5 years ago by ▴ 10
0
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1
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1.3k
views
PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
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votes
1
reply
1.0k
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
6.0 years ago twtoal ▴ 10
2
votes
5
replies
2.9k
views
Issue with BiocParallel
purecn biocparallel
6.1 years ago milos-91 • 0
0
votes
1
reply
1.0k
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
0
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3
replies
1.3k
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Assigning DUP/DEL p-value to CNV segment
PureCN
6.1 years ago twtoal ▴ 10
0
votes
1
reply
1.2k
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
6.1 years ago twtoal ▴ 10
0
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1
reply
1.2k
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
6.1 years ago twtoal ▴ 10
0
votes
2
replies
1.4k
views
CNV in Normal Samples?
PureCN Germline Normal CNV
updated 6.2 years ago by ▴ 130 • written 6.2 years ago by ▴ 10
1
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1
reply
1.0k
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
votes
1
reply
903
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
1
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3
replies
1.2k
views
PureCN Manual Curation .rds file
PureCN rds_file manual_curation
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
votes
4
replies
1.6k
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 6.3 years ago by ▴ 130 • written 6.3 years ago by ▴ 10
0
votes
3
replies
2.1k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
6.4 years ago • updated 6.3 years ago twtoal ▴ 10
0
votes
1
reply
1.4k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
6.4 years ago twtoal ▴ 10
0
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6
replies
2.0k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
6.5 years ago skkujin • 0
0
votes
5
replies
2.1k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 6.5 years ago by ▴ 130 • written 6.5 years ago by ▴ 10
3
votes
5
replies
1.9k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 6.5 years ago by • 0 • written 6.6 years ago by ▴ 10
0
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1
reply
1.1k
views
Is C adjusted for purity?
PureCN Adjusted C
updated 6.5 years ago by ▴ 130 • written 6.5 years ago by ▴ 10
0
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9
replies
2.0k
views
Unable to find solution: low coverage
PureCN fatal error no solution
6.5 years ago twtoal ▴ 10
0
votes
2
replies
993
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 6.5 years ago by ▴ 130 • written 6.5 years ago by ▴ 10
0
votes
4
replies
1.4k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
6.5 years ago twtoal ▴ 10
0
votes
6
replies
1.5k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
6.5 years ago twtoal ▴ 10
0
votes
2
replies
1.6k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
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4
replies
1.4k
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN Somatic Mutations
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
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2
replies
1.1k
views
Dx.R somatic_ontarget column
PureCN
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
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1
reply
1.1k
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
1
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3
replies
1.1k
views
PureCN Release Notes
PureCN Release
updated 6.6 years ago by 67k • written 6.6 years ago by ▴ 10
0
votes
1
reply
2.0k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
votes
3
replies
1.2k
views
PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
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4
replies
1.6k
views
PureCN error: zero-length 'labels' specified
PureCN
6.6 years ago twtoal ▴ 10
0
votes
1
reply
926
views
PureCN Panel of Normals contents
PureCN
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
votes
2
replies
1.1k
views
No CNAs or SNVs in results
PureCN
6.6 years ago twtoal ▴ 10
1
vote
1
reply
1.2k
views
PureCN support for indels
PureCN indels
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
votes
9
replies
1.7k
views
errors in version 1.7.53
PureCN
updated 7.1 years ago by ▴ 130 • written 7.1 years ago by • 0
0
votes
1
reply
1.2k
views
errors in Purecn callLOH
PureCN
updated 7.2 years ago by ▴ 130 • written 7.2 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 870
You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…
Answer: Identical samples after deseq2 batch effect removal by maripane • 0
Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…
Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0
The updated version worked well on my data. Thank you!
Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di by James W. MacDonald 67k
The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…
Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k
Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…
Votes
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
A: TopGO: How to retrieve the gene list related to a GO ID ?
A: Error in DESeqDataSet : some values in assay are not integers
A: correcting the batch effects in Limma and SVA
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