Showing : purecn • reset
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BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN biomaRt
updated 11 months ago by • 0 • written 13 months ago by • 0
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0
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1.2k
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Calculating tumour purity having only CNA data
PureCN CNA purity cancer
3.3 years ago JAcky • 0
1
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5
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2.6k
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Mutect version, matched normal and manual curation in PureCN
PureCN
3.3 years ago • updated 2.7 years ago Ken C • 0
1
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8
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2.3k
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PureCN: Copy Number of 7 issue
Pure PureCN
updated 3.9 years ago by ▴ 130 • written 3.9 years ago by • 0
1
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5
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2.1k
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PureCN C (integer segment copy number) in curated samples
PureC PureCN
updated 3.9 years ago by ▴ 130 • written 3.9 years ago by ▴ 10
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2
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1.5k
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PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 4.1 years ago by ▴ 130 • written 4.1 years ago by ▴ 10
0
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1
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1.1k
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PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 4.2 years ago by ▴ 130 • written 4.2 years ago by ▴ 10
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3
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1.4k
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Corrupt data in Sex column of .csv file
PureCN
4.4 years ago twtoal ▴ 10
0
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2
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2.0k
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PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
5.3 years ago twtoal ▴ 10
0
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3
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1.8k
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PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 5.4 years ago by ▴ 130 • written 5.4 years ago by ▴ 10
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4
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1.5k
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Why is PureCN LOH file missing some segments
purecn loh
5.6 years ago twtoal ▴ 10
0
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1
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1.2k
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 5.8 years ago by ▴ 130 • written 5.8 years ago by • 0
0
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2
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1.6k
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PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 5.9 years ago by ★ 6.6k • written 5.9 years ago by ▴ 10
0
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3
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1.4k
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callLOH output file NA values
PureCN NA values
updated 6.4 years ago by ▴ 130 • written 6.4 years ago by ▴ 10
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1
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1.5k
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PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 6.5 years ago by ▴ 130 • written 6.5 years ago by ▴ 10
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1
reply
1.2k
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Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
6.9 years ago twtoal ▴ 10
2
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5
replies
3.4k
views
Issue with BiocParallel
purecn biocparallel
7.0 years ago milos-91 • 0
0
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1
reply
1.3k
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 7.0 years ago by ▴ 130 • written 7.0 years ago by ▴ 10
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3
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1.6k
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Assigning DUP/DEL p-value to CNV segment
PureCN
7.0 years ago twtoal ▴ 10
0
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1
reply
1.4k
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 7.0 years ago by ▴ 130 • written 7.0 years ago by ▴ 10
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2
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1.3k
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
7.0 years ago twtoal ▴ 10
0
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1
reply
1.4k
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PureCN Solution Heatmap values
PureCN heatmap likelihoods
7.0 years ago twtoal ▴ 10
0
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2
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1.8k
views
CNV in Normal Samples?
PureCN Germline Normal CNV
updated 7.1 years ago by ▴ 130 • written 7.1 years ago by ▴ 10
1
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1
reply
1.2k
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 7.1 years ago by ▴ 130 • written 7.1 years ago by ▴ 10
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1
reply
1.1k
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 7.1 years ago by ▴ 130 • written 7.1 years ago by ▴ 10
1
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3
replies
1.6k
views
PureCN Manual Curation .rds file
PureCN rds_file manual_curation
updated 7.1 years ago by ▴ 130 • written 7.1 years ago by ▴ 10
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4
replies
1.9k
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PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 7.1 years ago by ▴ 130 • written 7.1 years ago by ▴ 10
0
votes
3
replies
2.4k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
7.3 years ago • updated 7.2 years ago twtoal ▴ 10
0
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1
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1.7k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
7.3 years ago twtoal ▴ 10
0
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6
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2.4k
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How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
7.3 years ago skkujin • 0
0
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5
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2.5k
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Is mean adjusted for purity?
PureCN mean ratio
updated 7.4 years ago by ▴ 130 • written 7.4 years ago by ▴ 10
3
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5
replies
2.3k
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Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 7.4 years ago by • 0 • written 7.5 years ago by ▴ 10
0
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1
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1.3k
views
Is C adjusted for purity?
PureCN Adjusted C
updated 7.4 years ago by ▴ 130 • written 7.4 years ago by ▴ 10
0
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9
replies
2.6k
views
Unable to find solution: low coverage
PureCN fatal error no solution
7.4 years ago twtoal ▴ 10
0
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2
replies
1.2k
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 7.4 years ago by ▴ 130 • written 7.4 years ago by ▴ 10
0
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4
replies
1.8k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN Purity Low Purity CNV
7.4 years ago twtoal ▴ 10
0
votes
6
replies
1.9k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
7.4 years ago twtoal ▴ 10
0
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2
replies
1.9k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 7.4 years ago by ▴ 130 • written 7.4 years ago by ▴ 10
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4
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1.8k
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PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN Somatic Mutations
updated 7.4 years ago by ▴ 130 • written 7.4 years ago by ▴ 10
0
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2
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1.3k
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Dx.R somatic_ontarget column
PureCN
updated 7.4 years ago by ▴ 130 • written 7.4 years ago by ▴ 10
0
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1
reply
1.3k
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 7.4 years ago by ▴ 130 • written 7.5 years ago by ▴ 10
1
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3
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1.3k
views
PureCN Release Notes
PureCN Release
updated 7.5 years ago by 68k • written 7.5 years ago by ▴ 10
0
votes
1
reply
2.3k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 7.5 years ago by ▴ 130 • written 7.5 years ago by ▴ 10
0
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3
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1.4k
views
PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 7.5 years ago by ▴ 130 • written 7.5 years ago by ▴ 10
0
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4
replies
1.9k
views
PureCN error: zero-length 'labels' specified
PureCN
7.5 years ago twtoal ▴ 10
0
votes
1
reply
1.1k
views
PureCN Panel of Normals contents
PureCN
updated 7.5 years ago by ▴ 130 • written 7.5 years ago by ▴ 10
0
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2
replies
1.4k
views
No CNAs or SNVs in results
PureCN
7.5 years ago twtoal ▴ 10
1
vote
1
reply
1.4k
views
PureCN support for indels
PureCN indels
updated 7.5 years ago by ▴ 130 • written 7.5 years ago by ▴ 10
0
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9
replies
2.1k
views
errors in version 1.7.53
PureCN
updated 8.0 years ago by ▴ 130 • written 8.0 years ago by • 0
0
votes
1
reply
1.4k
views
errors in Purecn callLOH
PureCN
updated 8.0 years ago by ▴ 130 • written 8.0 years ago by • 0
55 results • Page 1 of 2
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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