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purecn
•
reset
0
votes
0
replies
790
views
Calculating tumour purity having only CNA data
PureCN
CNA
purity
cancer
2.0 years ago
JAcky
• 0
1
vote
5
replies
1.7k
views
Mutect version, matched normal and manual curation in PureCN
PureCN
2.1 years ago • updated 17 months ago
Ken C
• 0
1
vote
8
replies
1.6k
views
PureCN: Copy Number of 7 issue
Pure
PureCN
updated 2.6 years ago by
markus.riester
▴ 130 • written 2.6 years ago by
jacobgross04
• 0
1
vote
5
replies
1.4k
views
PureCN C (integer segment copy number) in curated samples
PureC
PureCN
updated 2.6 years ago by
markus.riester
▴ 130 • written 2.6 years ago by
twtoal
▴ 10
0
votes
2
replies
1.0k
views
PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN
COSMIC
updated 2.8 years ago by
markus.riester
▴ 130 • written 2.8 years ago by
twtoal
▴ 10
0
votes
1
reply
765
views
PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation
GermlineMutation
PureCN
updated 2.9 years ago by
markus.riester
▴ 130 • written 2.9 years ago by
twtoal
▴ 10
0
votes
3
replies
924
views
Corrupt data in Sex column of .csv file
PureCN
3.2 years ago
twtoal
▴ 10
0
votes
2
replies
1.3k
views
PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN
ASCAT
purity
ploidy
multi-regional sequencing
4.0 years ago
twtoal
▴ 10
0
votes
3
replies
1.1k
views
PureCN gene LOH very common, amp/del not
PureCN
gene
amplification
deletion
loh
updated 4.1 years ago by
markus.riester
▴ 130 • written 4.1 years ago by
twtoal
▴ 10
0
votes
4
replies
1.0k
views
Why is PureCN LOH file missing some segments
purecn
loh
4.3 years ago
twtoal
▴ 10
0
votes
1
reply
840
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN
CNV
CNA
segmentation
calculateTangentNormal
updated 4.6 years ago by
markus.riester
▴ 130 • written 4.6 years ago by
sruddy17
• 0
0
votes
2
replies
1.2k
views
PureCN version clashes at GitHub and Bioconductor
version
PureCN
updated 4.6 years ago by
Mike Smith
★ 6.5k • written 4.6 years ago by
twtoal
▴ 10
0
votes
3
replies
957
views
callLOH output file NA values
PureCN
NA values
updated 5.2 years ago by
markus.riester
▴ 130 • written 5.2 years ago by
twtoal
▴ 10
0
votes
1
reply
1.1k
views
PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 5.2 years ago by
markus.riester
▴ 130 • written 5.2 years ago by
twtoal
▴ 10
0
votes
1
reply
913
views
Chromosome arm loss and --maxhomozygousloss default
Purecn
maxhomozygousloss
5.6 years ago
twtoal
▴ 10
2
votes
5
replies
2.7k
views
Issue with BiocParallel
purecn
biocparallel
5.7 years ago
milos-91
• 0
0
votes
1
reply
913
views
Copy ratio close to but not exactly 1
PureCN
CopyRatio
updated 5.7 years ago by
markus.riester
▴ 130 • written 5.7 years ago by
twtoal
▴ 10
0
votes
3
replies
1.2k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
5.7 years ago
twtoal
▴ 10
0
votes
1
reply
1.1k
views
Copy ratio threshold for calling actual CNV
PureCN
copy-ratio
threshold
updated 5.7 years ago by
markus.riester
▴ 130 • written 5.7 years ago by
twtoal
▴ 10
0
votes
2
replies
941
views
Mutation Burden file and manual curation
purecn
mutation_burden
manual_curation
5.8 years ago
twtoal
▴ 10
0
votes
1
reply
1.1k
views
PureCN Solution Heatmap values
PureCN
heatmap
likelihoods
5.8 years ago
twtoal
▴ 10
0
votes
2
replies
1.2k
views
CNV in Normal Samples?
PureCN
Germline
Normal
CNV
updated 5.8 years ago by
markus.riester
▴ 130 • written 5.8 years ago by
twtoal
▴ 10
1
vote
1
reply
917
views
PureCN recover optimum solution
PureCN
Optimum_solution
updated 5.9 years ago by
markus.riester
▴ 130 • written 5.9 years ago by
twtoal
▴ 10
0
votes
1
reply
790
views
PureCN PureCN.R --rds option recreate all output files?
PureCN
--rds
updated 5.9 years ago by
markus.riester
▴ 130 • written 5.9 years ago by
twtoal
▴ 10
1
vote
3
replies
1.1k
views
PureCN Manual Curation .rds file
PureCN
rds_file
manual_curation
updated 5.9 years ago by
markus.riester
▴ 130 • written 5.9 years ago by
twtoal
▴ 10
0
votes
4
replies
1.4k
views
PureCN optimum solution vs heat map
PureCN
Solution
Heatmap
updated 5.9 years ago by
markus.riester
▴ 130 • written 5.9 years ago by
twtoal
▴ 10
0
votes
3
replies
1.9k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
6.0 years ago • updated 5.9 years ago
twtoal
▴ 10
0
votes
1
reply
1.2k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
6.0 years ago
twtoal
▴ 10
0
votes
6
replies
1.8k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
6.1 years ago
skkujin
• 0
0
votes
5
replies
1.9k
views
Is mean adjusted for purity?
PureCN
mean ratio
updated 6.1 years ago by
markus.riester
▴ 130 • written 6.1 years ago by
twtoal
▴ 10
3
votes
5
replies
1.7k
views
Understanding PureCN and its germline SNPs
PureCN
germline
SNP
updated 6.1 years ago by
kakbrus
• 0 • written 6.3 years ago by
twtoal
▴ 10
0
votes
1
reply
1.0k
views
Is C adjusted for purity?
PureCN
Adjusted C
updated 6.1 years ago by
markus.riester
▴ 130 • written 6.1 years ago by
twtoal
▴ 10
0
votes
9
replies
1.8k
views
Unable to find solution: low coverage
PureCN
fatal error
no solution
6.1 years ago
twtoal
▴ 10
0
votes
2
replies
906
views
PureCN removemapq0 parameter
PureCN
removemapq0
updated 6.1 years ago by
markus.riester
▴ 130 • written 6.1 years ago by
twtoal
▴ 10
0
votes
4
replies
1.3k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN
Purity
Low Purity
CNV
6.1 years ago
twtoal
▴ 10
0
votes
6
replies
1.3k
views
Private Germline Count is mostly 0
PureCN
private_germline
mutation_burden
6.1 years ago
twtoal
▴ 10
0
votes
2
replies
1.4k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN
VCF
QUAL
updated 6.2 years ago by
markus.riester
▴ 130 • written 6.2 years ago by
twtoal
▴ 10
0
votes
4
replies
1.2k
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN
Somatic Mutations
updated 6.2 years ago by
markus.riester
▴ 130 • written 6.2 years ago by
twtoal
▴ 10
0
votes
2
replies
967
views
Dx.R somatic_ontarget column
PureCN
updated 6.2 years ago by
markus.riester
▴ 130 • written 6.2 years ago by
twtoal
▴ 10
0
votes
1
reply
1.0k
views
coverage QC file mean duplication and "mom" columns
PureCN
coverage
updated 6.2 years ago by
markus.riester
▴ 130 • written 6.2 years ago by
twtoal
▴ 10
1
vote
3
replies
1000
views
PureCN Release Notes
PureCN
Release
updated 6.2 years ago by
James W. MacDonald
66k • written 6.2 years ago by
twtoal
▴ 10
0
votes
1
reply
1.9k
views
VCF file non-SNP germline mutations
PureCN
VCF
SNP
updated 6.2 years ago by
markus.riester
▴ 130 • written 6.2 years ago by
twtoal
▴ 10
0
votes
3
replies
1.0k
views
PureCN warning: test.num.copy outside recommended range
PureCN
Warning
updated 6.2 years ago by
markus.riester
▴ 130 • written 6.2 years ago by
twtoal
▴ 10
0
votes
4
replies
1.4k
views
PureCN error: zero-length 'labels' specified
PureCN
6.2 years ago
twtoal
▴ 10
0
votes
1
reply
824
views
PureCN Panel of Normals contents
PureCN
updated 6.2 years ago by
markus.riester
▴ 130 • written 6.2 years ago by
twtoal
▴ 10
0
votes
2
replies
1.0k
views
No CNAs or SNVs in results
PureCN
6.2 years ago
twtoal
▴ 10
1
vote
1
reply
1.0k
views
PureCN support for indels
PureCN
indels
updated 6.2 years ago by
markus.riester
▴ 130 • written 6.3 years ago by
twtoal
▴ 10
0
votes
9
replies
1.4k
views
errors in version 1.7.53
PureCN
updated 6.8 years ago by
markus.riester
▴ 130 • written 6.8 years ago by
xiao.qiao.liu
• 0
0
votes
1
reply
1.1k
views
errors in Purecn callLOH
PureCN
updated 6.8 years ago by
markus.riester
▴ 130 • written 6.8 years ago by
xiao.qiao.liu
• 0
2
votes
3
replies
1.2k
views
PureCN can classify indel variants as germline vs. somatic ?
PureCN
indel
somatic
germline
updated 7.1 years ago by
markus.riester
▴ 130 • written 7.1 years ago by
pathkim
• 0
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Comment: limma comparison for small sample size and how to get covariance matrix
by
Gordon Smyth
51k
Your MDS plot is better than before, but you are still not following the recommendation for making for making such plots given in the limma…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Also, ``` > result <- mapUniProt( from = "EMBL-GenBank-DDBJ_CDS", to = "UniProtKB", query = c("ACF95883.1") ) > result From…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Ugh, here's the link https://www.uniprot.org/id-mapping/uniprotkb/dd08aa16774d98ef087dc3bd708582012bba49e2/overview?fields=accession%2Cre…
Answer: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
The input should be 'EMBL-GenBank-DDBJ_CDS", as that is a GenBank ID.
Answer: XCMS2 of orbitrap data
by
Elodie
• 0
Hi, I have the same question, I have acquired MS2 data with PRM analysis and inclusion lists of several ions. I have a list of product ion…
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Answer: EPIC array hg38 annotation?
Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
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