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PureCN
•
reset
3
votes
5
replies
1.9k
views
Understanding PureCN and its germline SNPs
PureCN
germline
SNP
updated 6.5 years ago by
kakbrus
• 0 • written 6.7 years ago by
twtoal
▴ 10
2
votes
3
replies
1.4k
views
PureCN can classify indel variants as germline vs. somatic ?
PureCN
indel
somatic
germline
updated 7.5 years ago by
markus.riester
▴ 130 • written 7.5 years ago by
pathkim
• 0
2
votes
5
replies
2.9k
views
Issue with BiocParallel
purecn
biocparallel
6.1 years ago
milos-91
• 0
1
vote
1
reply
1.1k
views
Bug Report/Question for PureCN: createSNPBlacklist() Error
PureCN
updated 8.4 years ago by
markus.riester
▴ 130 • written 8.4 years ago by
klminch
▴ 10
1
vote
5
replies
1.7k
views
PureCN C (integer segment copy number) in curated samples
PureC
PureCN
updated 3.1 years ago by
markus.riester
▴ 130 • written 3.1 years ago by
twtoal
▴ 10
1
vote
3
replies
1.1k
views
PureCN Release Notes
PureCN
Release
updated 6.6 years ago by
James W. MacDonald
67k • written 6.6 years ago by
twtoal
▴ 10
1
vote
8
replies
1.9k
views
PureCN: Copy Number of 7 issue
Pure
PureCN
updated 3.0 years ago by
markus.riester
▴ 130 • written 3.0 years ago by
jacobgross04
• 0
1
vote
3
replies
1.3k
views
PureCN Manual Curation .rds file
PureCN
rds_file
manual_curation
updated 6.3 years ago by
markus.riester
▴ 130 • written 6.3 years ago by
twtoal
▴ 10
1
vote
1
reply
1.2k
views
PureCN support for indels
PureCN
indels
updated 6.7 years ago by
markus.riester
▴ 130 • written 6.7 years ago by
twtoal
▴ 10
1
vote
4
replies
806
views
BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN
biomaRt
updated 4 weeks ago by
Adam
• 0 • written 3 months ago by
varga.luca
• 0
1
vote
1
reply
1.0k
views
PureCN recover optimum solution
PureCN
Optimum_solution
updated 6.3 years ago by
markus.riester
▴ 130 • written 6.3 years ago by
twtoal
▴ 10
1
vote
5
replies
2.0k
views
Mutect version, matched normal and manual curation in PureCN
PureCN
2.5 years ago • updated 22 months ago
Ken C
• 0
0
votes
1
reply
1.1k
views
coverage QC file mean duplication and "mom" columns
PureCN
coverage
updated 6.6 years ago by
markus.riester
▴ 130 • written 6.6 years ago by
twtoal
▴ 10
0
votes
4
replies
1.4k
views
PureCN.R _variants.csv file prior.somatic and somatic variant count
PureCN
Somatic Mutations
updated 6.6 years ago by
markus.riester
▴ 130 • written 6.6 years ago by
twtoal
▴ 10
0
votes
2
replies
1.6k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN
VCF
QUAL
updated 6.6 years ago by
markus.riester
▴ 130 • written 6.6 years ago by
twtoal
▴ 10
0
votes
6
replies
1.5k
views
Private Germline Count is mostly 0
PureCN
private_germline
mutation_burden
6.6 years ago
twtoal
▴ 10
0
votes
4
replies
1.4k
views
Does Greater Depth Allow Low Purity To Work Well?
PureCN
Purity
Low Purity
CNV
6.6 years ago
twtoal
▴ 10
0
votes
2
replies
1.0k
views
PureCN removemapq0 parameter
PureCN
removemapq0
updated 6.6 years ago by
markus.riester
▴ 130 • written 6.6 years ago by
twtoal
▴ 10
0
votes
9
replies
2.1k
views
Unable to find solution: low coverage
PureCN
fatal error
no solution
6.6 years ago
twtoal
▴ 10
0
votes
1
reply
1.2k
views
Is C adjusted for purity?
PureCN
Adjusted C
updated 6.6 years ago by
markus.riester
▴ 130 • written 6.6 years ago by
twtoal
▴ 10
0
votes
5
replies
2.1k
views
Is mean adjusted for purity?
PureCN
mean ratio
updated 6.5 years ago by
markus.riester
▴ 130 • written 6.5 years ago by
twtoal
▴ 10
0
votes
6
replies
2.0k
views
How can I improve somatic/germline status prediction without matched normal (PureCN)?
purecn
6.5 years ago
skkujin
• 0
0
votes
1
reply
1.4k
views
PureCN Error in xg[1, ] : incorrect number of dimensions
PureCN
6.5 years ago
twtoal
▴ 10
0
votes
3
replies
2.1k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
6.5 years ago • updated 6.3 years ago
twtoal
▴ 10
0
votes
4
replies
1.6k
views
PureCN optimum solution vs heat map
PureCN
Solution
Heatmap
updated 6.3 years ago by
markus.riester
▴ 130 • written 6.3 years ago by
twtoal
▴ 10
0
votes
1
reply
908
views
PureCN PureCN.R --rds option recreate all output files?
PureCN
--rds
updated 6.3 years ago by
markus.riester
▴ 130 • written 6.3 years ago by
twtoal
▴ 10
0
votes
2
replies
1.4k
views
CNV in Normal Samples?
PureCN
Germline
Normal
CNV
updated 6.2 years ago by
markus.riester
▴ 130 • written 6.2 years ago by
twtoal
▴ 10
0
votes
1
reply
1.2k
views
PureCN Solution Heatmap values
PureCN
heatmap
likelihoods
6.2 years ago
twtoal
▴ 10
0
votes
2
replies
1.1k
views
Mutation Burden file and manual curation
purecn
mutation_burden
manual_curation
6.2 years ago
twtoal
▴ 10
0
votes
1
reply
1.2k
views
Copy ratio threshold for calling actual CNV
PureCN
copy-ratio
threshold
updated 6.2 years ago by
markus.riester
▴ 130 • written 6.2 years ago by
twtoal
▴ 10
0
votes
3
replies
1.3k
views
Assigning DUP/DEL p-value to CNV segment
PureCN
6.2 years ago
twtoal
▴ 10
0
votes
1
reply
1.0k
views
Copy ratio close to but not exactly 1
PureCN
CopyRatio
updated 6.1 years ago by
markus.riester
▴ 130 • written 6.2 years ago by
twtoal
▴ 10
0
votes
1
reply
1.0k
views
Chromosome arm loss and --maxhomozygousloss default
Purecn
maxhomozygousloss
6.0 years ago
twtoal
▴ 10
0
votes
1
reply
1.3k
views
PureCN.R warning "duplicate keys in header will be forced to unique rownames"
PureCN
updated 5.6 years ago by
markus.riester
▴ 130 • written 5.6 years ago by
twtoal
▴ 10
0
votes
3
replies
1.1k
views
callLOH output file NA values
PureCN
NA values
updated 5.6 years ago by
markus.riester
▴ 130 • written 5.6 years ago by
twtoal
▴ 10
0
votes
2
replies
1.4k
views
PureCN version clashes at GitHub and Bioconductor
version
PureCN
updated 5.0 years ago by
Mike Smith
★ 6.6k • written 5.0 years ago by
twtoal
▴ 10
0
votes
1
reply
967
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN
CNV
CNA
segmentation
calculateTangentNormal
updated 5.0 years ago by
markus.riester
▴ 130 • written 5.0 years ago by
sruddy17
• 0
0
votes
4
replies
1.2k
views
Why is PureCN LOH file missing some segments
purecn
loh
4.8 years ago
twtoal
▴ 10
0
votes
3
replies
1.4k
views
PureCN gene LOH very common, amp/del not
PureCN
gene
amplification
deletion
loh
updated 4.6 years ago by
markus.riester
▴ 130 • written 4.6 years ago by
twtoal
▴ 10
0
votes
2
replies
1.6k
views
PureCN/ASCAT comparison and purity/ploidy of multi-regional sequencing data
PureCN
ASCAT
purity
ploidy
multi-regional sequencing
4.5 years ago
twtoal
▴ 10
0
votes
3
replies
1.1k
views
Corrupt data in Sex column of .csv file
PureCN
3.6 years ago
twtoal
▴ 10
0
votes
2
replies
1.2k
views
PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN
COSMIC
updated 3.2 years ago by
markus.riester
▴ 130 • written 3.3 years ago by
twtoal
▴ 10
0
votes
0
replies
946
views
Calculating tumour purity having only CNA data
PureCN
CNA
purity
cancer
2.4 years ago
JAcky
• 0
0
votes
1
reply
896
views
PureCN performance of somatic/germline status prediction without matched normal?
SomaticMutation
GermlineMutation
PureCN
updated 3.3 years ago by
markus.riester
▴ 130 • written 3.3 years ago by
twtoal
▴ 10
0
votes
8
replies
1.8k
views
Error in running development version of PureCN
PureCN
software error
8.2 years ago
hustlxc
• 0
0
votes
1
reply
798
views
Error in running example code of PureCN
PureCN
updated 8.2 years ago by
markus.riester
▴ 130 • written 8.2 years ago by
rahulk.aiims
• 0
0
votes
1
reply
1.1k
views
how to make sure PureCN gets somatic status from VCF?
PureCN
updated 8.0 years ago by
markus.riester
▴ 130 • written 8.0 years ago by
eddieasalinas
• 0
0
votes
1
reply
1.2k
views
errors in Purecn callLOH
PureCN
updated 7.2 years ago by
markus.riester
▴ 130 • written 7.2 years ago by
xiao.qiao.liu
• 0
0
votes
9
replies
1.7k
views
errors in version 1.7.53
PureCN
updated 7.2 years ago by
markus.riester
▴ 130 • written 7.2 years ago by
xiao.qiao.liu
• 0
0
votes
2
replies
1.1k
views
No CNAs or SNVs in results
PureCN
6.6 years ago
twtoal
▴ 10
50 results • Page
1 of 1
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Answer: Advice needed: Using limma for differential pathway analysis with continuous dis
by
Gordon Smyth
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limma has always handled any combination of continuous or categorical variables from the very beginning. You simply add continuous variable…
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi @yangliao, thanks for the note. We use Feature Counts extensively for gene-level counting (exon features). Unfortunately though, and I…
Comment: Feature Counts - potential bug with outfile.jcounts
by
Yang Liao
▴ 450
When you use `featureCounts` to count junctions with the `-J` option, it doesn't check if the junction is exactly overlap with exons of gen…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
by
ATpoint
★ 4.6k
I think you run into the common pitfall that you treat results as categorical (significant, not significant) whereas in reality the results…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
by
swbarnes2
★ 1.4k
It would probably help if you broke out the raw and normalized read counts for all the samples.
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Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Comment: What type of counts data to import for performing Isoform analysis in edgeR
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