Showing : Purecn • reset
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Calculating tumour purity having only CNA data
PureCN CNA purity cancer
21 months ago JAcky • 0
1
vote
5
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1.5k
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Mutect version, matched normal and manual curation in PureCN
PureCN
22 months ago • updated 14 months ago Ken C • 0
1
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8
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1.5k
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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
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PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 2.4 years ago by ▴ 130 • written 2.4 years ago by ▴ 10
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2
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971
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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
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1
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684
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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
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3
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853
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Corrupt data in Sex column of .csv file
PureCN
3.0 years ago twtoal ▴ 10
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2
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1.1k
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PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
3.8 years ago twtoal ▴ 10
0
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3
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994
views
PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 3.9 years ago by ▴ 130 • written 3.9 years ago by ▴ 10
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4
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958
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Why is PureCN LOH file missing some segments
purecn loh
4.1 years ago twtoal ▴ 10
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1
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779
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PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 4.3 years ago by ▴ 130 • written 4.3 years ago by • 0
0
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2
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1.1k
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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
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3
replies
892
views
callLOH output file NA values
PureCN NA values
updated 4.9 years ago by ▴ 130 • written 4.9 years ago by ▴ 10
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1
reply
1000
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
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1
reply
865
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Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
5.4 years ago twtoal ▴ 10
2
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5
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2.5k
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Issue with BiocParallel
purecn biocparallel
5.5 years ago milos-91 • 0
0
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1
reply
862
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
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3
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1.1k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
5.5 years ago twtoal ▴ 10
0
votes
1
reply
997
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 5.5 years ago by ▴ 130 • written 5.5 years ago by ▴ 10
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2
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888
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Mutation Burden file and manual curation
purecn mutation_burden manual_curation
5.5 years ago twtoal ▴ 10
0
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1
reply
995
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
5.5 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
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1
reply
852
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
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1
reply
738
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
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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
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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
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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
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1
reply
1.1k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
5.8 years ago twtoal ▴ 10
0
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6
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1.6k
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How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
5.9 years ago skkujin • 0
0
votes
5
replies
1.7k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
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1
reply
948
views
Is C adjusted for purity?
PureCN Adjusted C
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
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9
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1.6k
views
Unable to find solution: low coverage
PureCN fatal error no solution
5.9 years ago twtoal ▴ 10
0
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2
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864
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
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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
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6
replies
1.3k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
5.9 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
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4
replies
1.1k
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
903
views
Dx.R somatic_ontarget column
PureCN
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
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1
reply
976
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
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3
replies
938
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PureCN Release Notes
PureCN Release
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 10
0
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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
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3
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967
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
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4
replies
1.3k
views
PureCN error: zero-length 'labels' specified
PureCN
6.0 years ago twtoal ▴ 10
0
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1
reply
774
views
PureCN Panel of Normals contents
PureCN
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
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2
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974
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No CNAs or SNVs in results
PureCN
6.0 years ago twtoal ▴ 10
3
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5
replies
1.6k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 5.9 years ago by • 0 • written 6.0 years ago by ▴ 10
1
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1
reply
936
views
PureCN support for indels
PureCN indels
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
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9
replies
1.4k
views
errors in version 1.7.53
PureCN
updated 6.5 years ago by ▴ 130 • written 6.5 years ago by • 0
0
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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
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Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts by Michael Love 41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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