Showing : PureCN • reset
0
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8
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2.1k
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Error in running development version of PureCN
PureCN software error
9.2 years ago hustlxc • 0
3
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5
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2.4k
views
Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 7.6 years ago by • 0 • written 7.7 years ago by ▴ 10
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2
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1.6k
views
PureCN version clashes at GitHub and Bioconductor
version PureCN
updated 6.1 years ago by ★ 6.6k • written 6.1 years ago by ▴ 10
0
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4
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1.9k
views
PureCN error: zero-length 'labels' specified
PureCN
7.6 years ago twtoal ▴ 10
0
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2
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1.4k
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Mutation Burden file and manual curation
purecn mutation_burden manual_curation
7.2 years ago twtoal ▴ 10
0
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9
replies
2.1k
views
errors in version 1.7.53
PureCN
updated 8.2 years ago by ▴ 130 • written 8.2 years ago by • 0
1
vote
1
reply
1.5k
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PureCN support for indels
PureCN indels
updated 7.7 years ago by ▴ 130 • written 7.7 years ago by ▴ 10
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2
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1.4k
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No CNAs or SNVs in results
PureCN
7.6 years ago twtoal ▴ 10
0
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1
reply
1.2k
views
PureCN Panel of Normals contents
PureCN
updated 7.6 years ago by ▴ 130 • written 7.6 years ago by ▴ 10
0
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2
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1.4k
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Dx.R somatic_ontarget column
PureCN
updated 7.6 years ago by ▴ 130 • written 7.6 years ago by ▴ 10
0
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3
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1.4k
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PureCN warning: test.num.copy outside recommended range
PureCN Warning
updated 7.6 years ago by ▴ 130 • written 7.6 years ago by ▴ 10
0
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1
reply
2.3k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 7.6 years ago by ▴ 130 • written 7.6 years ago by ▴ 10
1
vote
3
replies
1.4k
views
PureCN Release Notes
PureCN Release
updated 7.6 years ago by 68k • written 7.6 years ago by ▴ 10
0
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1
reply
1.3k
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coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 7.6 years ago by ▴ 130 • written 7.6 years ago by ▴ 10
0
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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 7.6 years ago by ▴ 130 • written 7.6 years ago by ▴ 10
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2
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2.0k
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PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 7.6 years ago by ▴ 130 • written 7.6 years ago by ▴ 10
0
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6
replies
2.0k
views
Private Germline Count is mostly 0
PureCN private_germline mutation_burden
7.6 years ago twtoal ▴ 10
0
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2
replies
1.2k
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 7.6 years ago by ▴ 130 • written 7.6 years ago by ▴ 10
0
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1
reply
1.4k
views
Is C adjusted for purity?
PureCN Adjusted C
updated 7.6 years ago by ▴ 130 • written 7.6 years ago by ▴ 10
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5
replies
2.6k
views
Is mean adjusted for purity?
PureCN mean ratio
updated 7.6 years ago by ▴ 130 • written 7.6 years ago by ▴ 10
1
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4
replies
1.9k
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BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN biomaRt
updated 13 months ago by • 0 • written 15 months ago by • 0
0
votes
1
reply
974
views
Error in running example code of PureCN
PureCN
updated 9.2 years ago by ▴ 130 • written 9.2 years ago by • 0
0
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1
reply
1.4k
views
how to make sure PureCN gets somatic status from VCF?
PureCN
updated 9.0 years ago by ▴ 130 • written 9.0 years ago by • 0
2
votes
3
replies
1.7k
views
PureCN can classify indel variants as germline vs. somatic ?
PureCN indel somatic germline
updated 8.5 years ago by ▴ 130 • written 8.5 years ago by • 0
0
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1
reply
1.5k
views
errors in Purecn callLOH
PureCN
updated 8.2 years ago by ▴ 130 • written 8.2 years ago by • 0
0
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3
replies
1.5k
views
callLOH output file NA values
PureCN NA values
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
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1
reply
1.2k
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN CNV CNA segmentation calculateTangentNormal
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by • 0
0
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4
replies
1.6k
views
Why is PureCN LOH file missing some segments
purecn loh
5.8 years ago twtoal ▴ 10
0
votes
3
replies
1.9k
views
PureCN gene LOH very common, amp/del not
PureCN gene amplification deletion loh
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
0
votes
1
reply
1.2k
views
PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation GermlineMutation PureCN
updated 4.3 years ago by ▴ 130 • written 4.3 years ago by ▴ 10
0
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3
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1.4k
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Corrupt data in Sex column of .csv file
PureCN
4.6 years ago twtoal ▴ 10
1
vote
8
replies
2.5k
views
PureCN: Copy Number of 7 issue
Pure PureCN
updated 4.0 years ago by ▴ 130 • written 4.0 years ago by • 0
0
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2
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1.6k
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PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN COSMIC
updated 4.3 years ago by ▴ 130 • written 4.3 years ago by ▴ 10
1
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1
reply
1.3k
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Bug Report/Question for PureCN: createSNPBlacklist() Error
PureCN
updated 9.5 years ago by ▴ 130 • written 9.5 years ago by ▴ 10
0
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3
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2.5k
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PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
7.5 years ago • updated 7.3 years ago twtoal ▴ 10
0
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4
replies
2.0k
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PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 7.3 years ago by ▴ 130 • written 7.3 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 7.3 years ago by ▴ 130 • written 7.3 years ago by ▴ 10
0
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1
reply
1.1k
views
PureCN PureCN.R --rds option recreate all output files?
PureCN --rds
updated 7.3 years ago by ▴ 130 • written 7.3 years ago by ▴ 10
1
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1
reply
1.3k
views
PureCN recover optimum solution
PureCN Optimum_solution
updated 7.3 years ago by ▴ 130 • written 7.3 years ago by ▴ 10
0
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2
replies
1.8k
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CNV in Normal Samples?
PureCN Germline Normal CNV
updated 7.2 years ago by ▴ 130 • written 7.2 years ago by ▴ 10
0
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1
reply
1.5k
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
7.2 years ago twtoal ▴ 10
0
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1
reply
1.5k
views
Copy ratio threshold for calling actual CNV
PureCN copy-ratio threshold
updated 7.2 years ago by ▴ 130 • written 7.2 years ago by ▴ 10
0
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3
replies
1.8k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
7.2 years ago twtoal ▴ 10
0
votes
1
reply
1.4k
views
Copy ratio close to but not exactly 1
PureCN CopyRatio
updated 7.2 years ago by ▴ 130 • written 7.2 years ago by ▴ 10
0
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1
reply
1.3k
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
7.0 years ago twtoal ▴ 10
0
votes
1
reply
1.6k
views
PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 6.6 years ago by ▴ 130 • written 6.6 years ago by ▴ 10
0
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6
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2.6k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
7.5 years ago skkujin • 0
0
votes
1
reply
1.7k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
7.5 years ago twtoal ▴ 10
0
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9
replies
2.7k
views
Unable to find solution: low coverage
PureCN fatal error no solution
7.6 years ago twtoal ▴ 10
0
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2
replies
2.1k
views
PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN ASCAT purity ploidy multi-regional sequencing
5.5 years ago twtoal ▴ 10
55 results • Page 1 of 2
Recent ...
Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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