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Showing :
purecn
•
reset
2
votes
5
replies
2.5k
views
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
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
0
votes
5
replies
1.7k
views
Is mean adjusted for purity?
PureCN
mean ratio
updated 5.9 years ago by
markus.riester
▴ 130 • written 5.9 years ago by
twtoal
▴ 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
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
kakbrus
• 0 • written 6.0 years ago by
twtoal
▴ 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
markus.riester
▴ 130 • written 2.4 years ago by
jacobgross04
• 0
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
9
replies
1.4k
views
errors in version 1.7.53
PureCN
updated 6.5 years ago by
markus.riester
▴ 130 • written 6.5 years ago by
xiao.qiao.liu
• 0
0
votes
4
replies
1.3k
views
PureCN optimum solution vs heat map
PureCN
Solution
Heatmap
updated 5.7 years ago by
markus.riester
▴ 130 • written 5.7 years ago by
twtoal
▴ 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
markus.riester
▴ 130 • written 2.4 years ago by
twtoal
▴ 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
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 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
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
markus.riester
▴ 130 • written 6.9 years ago by
pathkim
• 0
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
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 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
markus.riester
▴ 130 • written 5.6 years ago by
twtoal
▴ 10
0
votes
2
replies
1.1k
views
PureCN version clashes at GitHub and Bioconductor
version
PureCN
updated 4.4 years ago by
Mike Smith
★ 6.5k • written 4.4 years ago by
twtoal
▴ 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
markus.riester
▴ 130 • written 6.6 years ago by
xiao.qiao.liu
• 0
1
vote
3
replies
1.0k
views
PureCN Manual Curation .rds file
PureCN
rds_file
manual_curation
updated 5.7 years ago by
markus.riester
▴ 130 • written 5.7 years ago by
twtoal
▴ 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
markus.riester
▴ 130 • written 5.0 years ago by
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
markus.riester
▴ 130 • written 5.5 years ago by
twtoal
▴ 10
0
votes
1
reply
997
views
PureCN Solution Heatmap values
PureCN
heatmap
likelihoods
5.6 years ago
twtoal
▴ 10
0
votes
3
replies
995
views
PureCN gene LOH very common, amp/del not
PureCN
gene
amplification
deletion
loh
updated 3.9 years ago by
markus.riester
▴ 130 • written 3.9 years ago by
twtoal
▴ 10
0
votes
1
reply
978
views
coverage QC file mean duplication and "mom" columns
PureCN
coverage
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
0
votes
2
replies
975
views
No CNAs or SNVs in results
PureCN
6.0 years ago
twtoal
▴ 10
0
votes
2
replies
974
views
PureCN COSMIC VCF via PureCN.R - is there an option?
PureCN
COSMIC
updated 2.6 years ago by
markus.riester
▴ 130 • written 2.6 years ago by
twtoal
▴ 10
0
votes
3
replies
968
views
PureCN warning: test.num.copy outside recommended range
PureCN
Warning
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
0
votes
4
replies
960
views
Why is PureCN LOH file missing some segments
purecn
loh
4.1 years ago
twtoal
▴ 10
0
votes
1
reply
950
views
how to make sure PureCN gets somatic status from VCF?
PureCN
updated 7.4 years ago by
markus.riester
▴ 130 • written 7.4 years ago by
eddieasalinas
• 0
0
votes
1
reply
949
views
Is C adjusted for purity?
PureCN
Adjusted C
updated 5.9 years ago by
markus.riester
▴ 130 • written 5.9 years ago by
twtoal
▴ 10
1
vote
1
reply
938
views
PureCN support for indels
PureCN
indels
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
1
vote
3
replies
938
views
PureCN Release Notes
PureCN
Release
updated 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
twtoal
▴ 10
1
vote
1
reply
919
views
Bug Report/Question for PureCN: createSNPBlacklist() Error
PureCN
updated 7.8 years ago by
markus.riester
▴ 130 • written 7.8 years ago by
klminch
▴ 10
0
votes
2
replies
904
views
Dx.R somatic_ontarget column
PureCN
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
0
votes
3
replies
893
views
callLOH output file NA values
PureCN
NA values
updated 5.0 years ago by
markus.riester
▴ 130 • written 5.0 years ago by
twtoal
▴ 10
0
votes
2
replies
891
views
Mutation Burden file and manual curation
purecn
mutation_burden
manual_curation
5.5 years ago
twtoal
▴ 10
0
votes
1
reply
869
views
Chromosome arm loss and --maxhomozygousloss default
Purecn
maxhomozygousloss
5.4 years ago
twtoal
▴ 10
0
votes
1
reply
867
views
Copy ratio close to but not exactly 1
PureCN
CopyRatio
updated 5.5 years ago by
markus.riester
▴ 130 • written 5.5 years ago by
twtoal
▴ 10
0
votes
2
replies
865
views
PureCN removemapq0 parameter
PureCN
removemapq0
updated 5.9 years ago by
markus.riester
▴ 130 • written 5.9 years ago by
twtoal
▴ 10
0
votes
3
replies
857
views
Corrupt data in Sex column of .csv file
PureCN
3.0 years ago
twtoal
▴ 10
1
vote
1
reply
855
views
PureCN recover optimum solution
PureCN
Optimum_solution
updated 5.7 years ago by
markus.riester
▴ 130 • written 5.7 years ago by
twtoal
▴ 10
0
votes
1
reply
781
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
markus.riester
▴ 130 • written 4.3 years ago by
sruddy17
• 0
0
votes
1
reply
775
views
PureCN Panel of Normals contents
PureCN
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Answer: Why p value inconsistent when using different number of pathway score?
by
ATpoint
★ 4.0k
Same answer as here: https://support.bioconductor.org/p/9157606/ Adding or removing data (samples, genes, pathways, observations...) chang…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
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