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lima1
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PureCN
Copy number calling and variant classification using targeted short read sequencing
https://bioconductor.org/packages/devel/bioc/html/PureCN.html
Artistic License 2.0
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PureCN-Steps
#370
ElhamJa63
opened
2 weeks ago
0
Error in h(simpleError(msg, call))
#369
kristianunger
closed
1 month ago
1
Question regrading the results
#368
maxanes
opened
1 month ago
0
PSCBS segmentation failed --> Error in write permission for R directory .cache
#367
lmanchon
closed
1 month ago
0
Issue 40
#366
lima1
closed
2 months ago
0
Issue 363
#365
lima1
closed
2 months ago
0
allelic copy number for segments
#364
jennyp76
opened
2 months ago
0
Small panel triggers an error in the `.getAverageWeightPV` function
#363
tinyheero
closed
2 months ago
3
Multi region curation
#362
jberg1999
closed
2 months ago
4
Single standard deviation vs. segment-centric standard deviation for logR likelihood
#361
tinyheero
closed
3 months ago
2
purity and ploidy corrected CN
#360
jennyp76
closed
2 months ago
7
Attempt in fixing #356.
#359
lima1
closed
3 months ago
0
WARN [2024-03-12 11:57:13] Could not find valid purity and ploidy solution. Error in results[[1]] : subscript out of bounds
#358
gagank4911
opened
3 months ago
0
Error: VCF either contains no germline variants or variants are not properly
#357
ShvartsmanIrina
closed
2 months ago
4
Seems forgotten assignmet operator
#356
sleyn
closed
3 months ago
2
Could not find valid purity and ploidy solution
#355
gagank4911
opened
4 months ago
0
Tumor only PureCN filtering failure
#354
Shenglai
closed
4 months ago
2
Question about different version.
#353
Shenglai
closed
4 months ago
9
HRD score from PureCN outputs
#352
ShvartsmanIrina
opened
4 months ago
2
how to improve detection of short CNV ?
#351
lmanchon
closed
4 months ago
12
Annotation using different database
#350
jennyp76
opened
5 months ago
1
Mismatch between tumor purity and number of copy number alterations
#349
gargid98
closed
4 months ago
1
IntervalFile.R
#348
gagank4911
closed
5 months ago
1
Question regarding the third-party segmentation file
#347
maxanes
closed
5 months ago
4
Commercial use of PureCN
#346
jennyp76
closed
5 months ago
3
Applicable for WES (not hybridization capture)
#345
jennyp76
closed
5 months ago
1
plotting error with cell line samples and --min-purity 0.98 --max-purity 0.99
#344
ThomasGro
closed
5 months ago
4
GATK segmentation might fail when all variants on a chromosome are filtered out.
#343
lima1
opened
5 months ago
0
Support for non-diploid allosome alterations
#342
lima1
opened
5 months ago
0
Running PureCN with only one normal samples
#341
sleyn
opened
6 months ago
1
question about cfDNA run
#340
maxanes
closed
6 months ago
3
Error with overlapping gaps when running PureCN
#339
akaviaLab
opened
6 months ago
6
In case this may be of help
#338
GuidoLeoni
opened
6 months ago
0
Remove superfluous condition statement on existence of vcf parameter in segmentationPSCBS
#337
tinyheero
closed
6 months ago
1
[PON] The normal.panel.vcf.file contains only a single sample
#336
mazzalab
closed
6 months ago
4
Return the exon.lrs variable to the returned list object of runAbsoluteCN()
#335
tinyheero
closed
7 months ago
3
Installation error
#334
mazzalab
closed
7 months ago
3
Attempt in making current developer version of GenomicsDB-R work.
#333
lima1
closed
7 months ago
0
PureCN.R returns many warnings. Possible issue with Panel of Normals.
#332
alextrouerntrend
closed
7 months ago
2
Missing chromosomename prefix in DNAcopy output file after PSCBS
#331
ericblanc20
closed
8 months ago
2
How to cite in the manuscript if running PureCN with GATK segmentation
#330
WangKang-Leo
closed
9 months ago
3
PureCN writes only a fraction of the variants reported in vcf
#329
GuidoLeoni
closed
7 months ago
5
UMI affect on PureCN estimates
#328
waemm
closed
7 months ago
2
FFPE Tumor Samples: Poor Goodness of Fit
#327
Moe94
closed
7 months ago
1
Issue 320
#326
lima1
closed
9 months ago
0
Updated documentation and comments: --max-allele-counts, dbSNP member…
#325
ddrichel
closed
7 months ago
1
How to set up sex of PON
#324
lmanchon
closed
8 months ago
17
PureCN with ultra-deep sequenced plasma gene-panels
#323
RomainBosselut
closed
8 months ago
1
'long flag "seg-file" is invalid'
#322
h170607
closed
9 months ago
9
Effect of --max-copy-number parameter on purity/ploidy and copy number estimates
#321
ddrichel
closed
7 months ago
4
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