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im3sanger
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dndscv
dN/dS methods to quantify selection in cancer and somatic evolution
GNU General Public License v3.0
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Regarding Zero coding substitutions found in this dataset.
#52
SmritiChawla
closed
4 years ago
2
Help troubleshooting global dn/ds
#51
njbernstein
closed
4 years ago
7
hg38 ref files
#50
alhafidzhamdan
closed
4 years ago
1
columns qmis_cv, qtrunc_cv, qallsubs_cv, pglobal_cv, qglobal_cv NA
#49
guidmt
closed
4 years ago
1
Error in names(x) <- value : 'names' attribute [10] must be the same length as the vector [9]
#48
carladosanjos
closed
4 years ago
2
Error in get(name, envir = asNamespace(pkg)
#47
natashiabo
closed
4 years ago
3
How could get NBR?
#46
ChongJenniferZhang
closed
4 years ago
3
Can this tool find dN/dS values within regions of a gene?
#45
programmingprincess
closed
4 years ago
1
theta.ml not converging
#44
vodkatad
closed
4 years ago
5
Zero coding substitutions found in this dataset
#43
huynguyen250896
closed
4 years ago
1
'closure error' plz help me.
#42
a00101
closed
4 years ago
1
Global dNdS ratios very high >1000
#41
tomsuntom
closed
4 years ago
2
Allow user to supply pre-loaded RefCDS-style object instead of file path
#40
jeff-mandell
closed
4 years ago
2
how to estimate probabilities that variants in particular exons ？
#39
feihongloveworld
closed
5 years ago
4
dndscv using MC3 maf file from TCGA
#38
KCLiv
closed
5 years ago
2
Interpretation of per-gene vs global dN/dS values
#37
JesseDGibson
closed
5 years ago
1
Help with trying to make a pentanucleotide substitution model
#36
arvindjs
closed
5 years ago
1
allow automatic installation of Bioconductor dependencies
#35
jeff-mandell
closed
5 years ago
2
DNDS-cv dropping lots of mutations
#34
ndfriedman
closed
5 years ago
4
how to convert gff3 to cdsfile for buildref
#33
starskyzheng
closed
5 years ago
1
RefCDS discrepancy when loading human GRCh38?
#32
Slavatron
closed
5 years ago
3
Fail to load Tutorial
#31
ChongJenniferZhang
closed
5 years ago
1
any plans to generate covariates for hg38?
#30
pwaltman
opened
5 years ago
12
compatibility with tibble
#29
ishida-md
closed
5 years ago
1
significant Q value with zero mutations
#28
emham
closed
5 years ago
3
Getting unkown error on my indel file
#27
beginner984
closed
5 years ago
1
Undefined column in running dndscv
#26
beginner984
closed
5 years ago
2
Unable to run dndscv
#25
beginner984
closed
5 years ago
5
Do I need these covariates for using dNdScv properly
#24
beginner984
closed
5 years ago
1
dndscv.R line 147, GenomicRanges::findOverlaps
#23
MaximilianStammnitz
closed
5 years ago
1
Positional shift if mutations$pos input column has factor levels
#22
MaximilianStammnitz
closed
5 years ago
1
RDA generation for new species crashes when exon boundary coincides with scaffold boundary
#21
MaximilianStammnitz
closed
5 years ago
3
Whole genome vs exome differences
#20
fpbarthel
closed
5 years ago
3
Question: dN/dS of 10
#19
zx8754
closed
5 years ago
2
Add chrom argument
#18
zx8754
closed
5 years ago
0
Different chromosome format in hg19 and hg38 rda file
#17
slzhao
closed
6 years ago
3
Support VCF as input?
#16
zx8754
closed
5 years ago
1
length(e1) not a multiple length(e2)
#15
fpbarthel
closed
6 years ago
10
Error in while ((it <- it + 1) < limit && abs(del) > eps) { : missing value where TRUE/FALSE needed
#14
AlfredShawn
closed
4 years ago
5
confidence intervals for gene-level dN/dS values and version for hg38
#13
AlinaSc
closed
6 years ago
1
No pglobal_cv and qglobal_cv in dndsout$sel_cv
#12
kmtiny
closed
6 years ago
2
Error in if (strand == 1) { : argument is of length zero
#11
adbeggs
closed
6 years ago
1
Error when using target sequencing sample
#10
Jingjiao-ma
closed
6 years ago
3
dndscv for other organisms
#9
sadafambreen
closed
6 years ago
8
Changed error to warning
#8
AJBerle
closed
6 years ago
2
Mutations observed in contiguous sites within a sample.
#7
madeleinedarbyshire
closed
6 years ago
5
Number of Driver Mutations
#6
madeleinedarbyshire
closed
6 years ago
1
Error using dndscv
#5
Salvobioinfo
closed
6 years ago
2
Error when using covariates
#4
pablo-gar
closed
6 years ago
6
other annotation file from hg19
#3
arpoe
closed
6 years ago
5
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