Showing : PureCN • reset
3
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5
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1.6k
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Understanding PureCN and its germline SNPs
PureCN germline SNP
updated 5.9 years ago by • 0 • written 6.0 years ago by ▴ 10
2
votes
5
replies
2.5k
views
Issue with BiocParallel
purecn biocparallel
5.5 years ago milos-91 • 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
1
vote
3
replies
938
views
PureCN Release Notes
PureCN Release
updated 6.0 years ago by 65k • written 6.0 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
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
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
1
vote
1
reply
935
views
PureCN support for indels
PureCN indels
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
1
vote
1
reply
916
views
Bug Report/Question for PureCN: createSNPBlacklist() Error
PureCN
updated 7.8 years ago by ▴ 130 • written 7.8 years ago by ▴ 10
1
vote
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
1
vote
5
replies
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
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
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
0
votes
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
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
votes
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
0
votes
2
replies
863
views
PureCN removemapq0 parameter
PureCN removemapq0
updated 5.9 years ago by ▴ 130 • written 5.9 years ago by ▴ 10
0
votes
9
replies
1.6k
views
Unable to find solution: low coverage
PureCN fatal error no solution
5.9 years ago twtoal ▴ 10
0
votes
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
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
1.6k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
5.9 years ago skkujin • 0
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
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
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
0
votes
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
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
1
reply
993
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
5.5 years ago twtoal ▴ 10
0
votes
2
replies
888
views
Mutation Burden file and manual curation
purecn mutation_burden manual_curation
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
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
861
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
1
reply
865
views
Chromosome arm loss and --maxhomozygousloss default
Purecn maxhomozygousloss
5.4 years ago twtoal ▴ 10
0
votes
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
0
votes
3
replies
891
views
callLOH output file NA values
PureCN NA values
updated 4.9 years ago by ▴ 130 • written 4.9 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
1
reply
779
views
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
votes
4
replies
957
views
Why is PureCN LOH file missing some segments
purecn loh
4.1 years ago twtoal ▴ 10
0
votes
3
replies
993
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
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
1
reply
684
views
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
0
votes
3
replies
853
views
Corrupt data in Sex column of .csv file
PureCN
3.0 years ago twtoal ▴ 10
0
votes
2
replies
971
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
0
replies
722
views
Calculating tumour purity having only CNA data
PureCN CNA purity cancer
21 months ago JAcky • 0
0
votes
8
replies
1.5k
views
Error in running development version of PureCN
PureCN software error
7.5 years ago hustlxc • 0
0
votes
1
reply
680
views
Error in running example code of PureCN
PureCN
updated 7.5 years ago by ▴ 130 • written 7.5 years ago by • 0
0
votes
1
reply
948
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
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
0
votes
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
votes
2
replies
974
views
No CNAs or SNVs in results
PureCN
6.0 years ago twtoal ▴ 10
50 results • Page 1 of 1
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Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by sredemption • 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…
Answer: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
The genes are automatically ordered within `fgsea`, there is no need to sort them manually.
Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Votes
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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