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mskcc
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facets
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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mm39 in the preProcSample {facets}
#200
karolina16
opened
1 week ago
1
Incorrect plots with purity=NA
#199
karolina16
closed
1 week ago
0
cf.em too low?
#198
THT-sleepy
opened
2 months ago
0
Can bams with marked duplicates(without removing) be used as input for snp-pileup?
#197
THT-sleepy
closed
2 months ago
0
snp_pileup returning no calls.
#196
apallav21
opened
5 months ago
0
What is difference between CNCF and EM plot/algorithm?
#195
allthetime115
opened
7 months ago
0
adding line in procSnps() to ensure required field order
#194
agorelick
opened
1 year ago
0
question about ploidy estimate
#193
guillaume-rs
opened
1 year ago
1
cf.em is NA
#192
rabiafidan
closed
1 year ago
5
run cnv_facets error for some samples, hope someone for help!!
#191
edceeyuchen
closed
1 year ago
1
properly order the jointseg
#190
ShixiangWang
opened
1 year ago
0
Impact of FFPE preservation
#189
mybabyfox
opened
1 year ago
0
Calling CNA from Cat genome; custom
#188
makarov-ccf
opened
1 year ago
3
Questions about ploidy estimate
#187
ysbioinfo
opened
1 year ago
0
pythonize snp-pileup
#186
veseshan
opened
1 year ago
0
the output description of the jointseg.txt
#185
litun-fkby
opened
1 year ago
0
Snp-pileup failed to return data
#184
boonhaohong
opened
1 year ago
8
fewer heterozygous variants
#183
jsha129
opened
1 year ago
4
Error "replacement has 0 rows", caused by dipLogR=numeric(0)
#182
ypradat
opened
1 year ago
2
Generat snplocs* files
#181
Jiayi-Wang-Joey
opened
1 year ago
0
Installation error
#180
Jiayi-Wang-Joey
opened
1 year ago
0
MacOS installation error | clang (LLVM option parsing): Unknown command line argument '-x86-pad-for-align=false'
#179
oliverartz
opened
1 year ago
2
purity is NA and how to interpret the plot
#178
stroke1989
opened
2 years ago
2
Add inst/CITATION + fix R CMD check errors
#177
HenrikBengtsson
opened
2 years ago
0
WISH: Add CITATION file => citation(package = "facets") mentions paper
#176
HenrikBengtsson
opened
2 years ago
0
only call individul normal bam
#175
gaom001
opened
2 years ago
0
Setting purity=1
#174
RoniHaas
closed
2 years ago
6
How the kernel density of cell fraction was plotted in the paper?
#173
zh9118
opened
2 years ago
2
Is tumor purity == 0.3 invalid?
#172
davidtourigny
opened
2 years ago
0
Purity NA - (with observed CN changes!)
#171
alexcoulton
opened
2 years ago
0
chromosome name
#170
sotaro-kanematsu
opened
2 years ago
1
FIX: Registration of the native API never took place
#169
HenrikBengtsson
closed
2 years ago
0
Tidy up package and enable CI checking on GitHub Actions
#168
HenrikBengtsson
closed
2 years ago
0
Yes "cnlr.median - dipLogR" is the log(total copy number) unadjusted for purity which is what you want.
#167
qindan2008
closed
2 years ago
0
how to install and use
#166
shujch
opened
2 years ago
3
WGS recommendations for chromothripsis analysis
#165
ahwanpandey
opened
2 years ago
0
Can not install using devtools
#164
jianxinwang
opened
2 years ago
1
ERROR happened in facets when calling CNV
#163
lizhan96
closed
3 years ago
0
Reduce memory usage of facets
#162
natir
opened
3 years ago
5
Facet bed: issue chromosomal position format
#161
legendre-adrien
opened
3 years ago
0
dependency pctGCdata has unclear requirements
#160
jbedo
closed
3 years ago
5
ndepth parameter for XX vs XY genome
#159
quentinba
opened
3 years ago
0
Comparing FACETS to results from callers that calculate a relative copy number only
#158
popicka
opened
3 years ago
0
ndepth in preProcSample is not suitable if can not be set as 0
#157
worker000000
opened
3 years ago
0
Can I force the ploidy to a specific value (experimentally validated) in facets?
#156
Francesc-Muyas
opened
3 years ago
0
emcncf called purity NA, ploidy 2, and em flag despite passing mafR.clust cutoff
#155
sas1531
opened
3 years ago
0
segclust Missing Error
#154
DarioS
opened
4 years ago
0
facets.R RAM issue
#153
alhafidzhamdan
opened
4 years ago
0
Weird regions of homozygous deletion
#152
af8
opened
4 years ago
0
snp-pileup compilation issue
#151
kibala93
opened
4 years ago
1
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