Showing : PureCN • reset
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
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
1.8k
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
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
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
9
replies
1.6k
views
Unable to find solution: low coverage
PureCN fatal error no solution
5.9 years ago twtoal ▴ 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
8
replies
1.5k
views
Error in running development version of PureCN
PureCN software error
7.5 years ago hustlxc • 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
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1.5k
views
Mutect version, matched normal and manual curation in PureCN
PureCN
22 months ago • updated 14 months ago Ken C • 0
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
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
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 2.4 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
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
5.9 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
5.9 years ago twtoal ▴ 10
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
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
1
reply
1.1k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
5.8 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
3.8 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
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
1.1k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
5.5 years ago twtoal ▴ 10
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
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
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
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
1000
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
5.6 years ago twtoal ▴ 10
0
votes
1
reply
998
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
0
votes
2
replies
979
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
979
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
2
replies
976
views
No CNAs or SNVs in results
PureCN
6.0 years ago twtoal ▴ 10
0
votes
3
replies
970
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
963
views
Why is PureCN LOH file missing some segments
purecn loh
4.1 years ago twtoal ▴ 10
0
votes
1
reply
953
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
1
reply
951
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
1
vote
3
replies
943
views
PureCN Release Notes
PureCN Release
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 10
1
vote
1
reply
941
views
PureCN support for indels
PureCN indels
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 10
1
vote
1
reply
924
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
2
replies
907
views
Dx.R somatic_ontarget column
PureCN
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
3
replies
900
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
2
replies
896
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
5.6 years ago twtoal ▴ 10
0
votes
1
reply
871
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
5.4 years ago twtoal ▴ 10
0
votes
1
reply
869
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
2
replies
866
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
1
vote
1
reply
862
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
0
votes
3
replies
860
views
Corrupt data in Sex column of .csv file
PureCN
3.0 years ago twtoal ▴ 10
0
votes
1
reply
786
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
1
reply
776
views
PureCN Panel of Normals contents
PureCN
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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