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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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calculation of dn/ds for bacterial genome data
#98
chantisakee
closed
5 days ago
2
Can we calculate dN/dS ratio for each sample?
#97
lincj1994
closed
2 months ago
1
can mutations contains indels?
#96
complexgenome
closed
3 months ago
1
using which refCDS-hg38? doubt for covariate
#95
complexgenome
closed
3 months ago
1
Error loading the hg38 reference database and the hg38 covariate files
#94
gat2010
opened
7 months ago
1
dndsout = dndscv(df) output error messages
#93
HendrinaS
closed
7 months ago
1
signif_genes = sel_cv[sel_cv$qglobal_cv<0.1, c("gene_name","qglobal_cv")] error
#92
HendrinaS
closed
1 year ago
1
question about confidence interval for INDELs
#91
loipf
opened
1 year ago
3
Zero values in some columns
#90
FL512
closed
1 year ago
1
Fix incorrect logic in line excluding non-synonymous mutations and those in known cancer genes.
#89
fitzlane86
opened
1 year ago
0
Problems encountered in using DNDSCV：[E::faidx_fetch_seq2] Failed to retrieve block. (Seeking in a compressed, .gzi unindexed, file?) Error in h(simpleError(msg, call)) : 在为'strsplit'函数选择方法时评估'x'参数出了错: record 1 (9:12285795-12285926) failed
#88
manchengyanyu
opened
1 year ago
0
Is there a way to change the omega(w) values
#87
ykginoue
closed
1 year ago
5
Arguments imply differing number of rows
#86
parvathisudha
closed
1 year ago
9
Error when trying to use buildref() : Error in new_codon[1, ]: incorrect number of dimensions
#85
tly0505
closed
1 year ago
1
How to verify the mutations are independent events?
#84
Sunsq1997
closed
1 year ago
1
Error in while ((it <- it + 1) < limit && abs(del) > eps)
#83
zhuhenan
closed
1 year ago
1
Could you add qind_cv to the output of sel_cv?
#82
njbernstein
closed
1 year ago
1
estimating global dNdSCV ratios from subsets of coding mutations
#81
bkinnersley
opened
2 years ago
2
The meaning of 'tml' in the 'dndscv.R'
#80
Sunsq1997
opened
2 years ago
0
dNdS script takes a lot of time to run
#79
sakrnference
closed
2 years ago
4
Handling of DBS
#78
ishida-md
closed
2 years ago
1
qglobal_cv of the top genes were zero.
#77
lincj1994
closed
1 year ago
1
5-nucleotide context mutational signature
#76
andreyurch
closed
2 years ago
1
Error when installing dndsv using: install_github("im3sanger/dndscv")
#75
sakrnference
closed
2 years ago
6
Apply dndscv to a Non-cancer population with high recombination
#74
huangl-CAU
closed
2 years ago
1
issue about position of input file
#73
stroke1989
closed
2 years ago
1
Normalize to depth of coverage across mitochondrial genome target?
#72
tessleuthner
closed
2 years ago
1
No qglobal_cv in "sel_cv"
#71
WangKang-Leo
closed
3 years ago
1
A wrong parameter in substmodel "192r_3w"?
#70
kakiuchi-kyt
closed
3 years ago
1
No genes with qglobal_cv < 0.1
#69
kvn95ss
opened
3 years ago
6
All the values of qglobal_cv are zero
#68
vivekruhela
closed
1 year ago
4
Didn't get pglobal_cv and qglobal_cv columns in the output file from the 1st step
#67
RupalHatkar
closed
3 years ago
3
Very high dnds values
#66
ArashDepp
closed
3 years ago
3
'Benjamini-Hodgberg' to 'Benjamini-Hochberg'
#65
rraadd88
opened
3 years ago
0
Interpreting dndscv results
#64
loukesio
closed
3 years ago
7
how to find genes with signature of purifying selection from dNdSCV results
#63
shaghayeghsoudi
closed
3 years ago
3
How to use dndscv in bacteria species?
#62
loukesio
closed
3 years ago
7
Fail to install
#61
missstcxq
closed
3 years ago
1
Zero coding substitutions found in this dataset
#60
eoinmck
closed
3 years ago
4
Build Ref error
#59
ggoodstudydaydayup
closed
3 years ago
1
fix im3sanger/dndscv#57
#58
luca-dex
opened
4 years ago
0
Name clash error on load
#57
luca-dex
opened
4 years ago
0
qglobal_cv and qallsubs_cv = 1
#56
antu2817
closed
4 years ago
2
Error in RefCDS[[j]] : subscript out of bounds
#55
CraigJAnderson
opened
4 years ago
2
Help troubleshooting metastasis analysis
#54
carladosanjos
closed
4 years ago
1
Can you explain mrfold?
#53
njbernstein
closed
4 years ago
1
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
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