im3sanger dndscv issues

im3sanger / dndscv

dN/dS methods to quantify selection in cancer and somatic evolution

GNU General Public License v3.0

212 stars 48 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Double base substitutions annotation

#102 andreyurch opened 2 weeks ago
0
Error for mitochondrial refcds

#101 moshl opened 2 weeks ago
0
Genes missing in hg38 ref file

#100 sahilseth opened 4 weeks ago
0
How do I run Duplex sequence results with dndscv/

#99 zongdawu opened 1 month ago
0
calculation of dn/ds for bacterial genome data

#98 chantisakee closed 1 month ago
2
Can we calculate dN/dS ratio for each sample?

#97 lincj1994 closed 4 months ago
1
can mutations contains indels?

#96 complexgenome closed 4 months ago
1
using which refCDS-hg38? doubt for covariate

#95 complexgenome closed 4 months ago
1
Error loading the hg38 reference database and the hg38 covariate files

#94 gat2010 opened 9 months ago
1
dndsout = dndscv(df) output error messages

#93 HendrinaS closed 9 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 2 years ago
1
Error in while ((it <- it + 1) < limit && abs(del) > eps)

#83 zhuhenan closed 2 years ago
1
Could you add qind_cv to the output of sel_cv?

#82 njbernstein closed 2 years 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 2 years 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 3 years ago
1
Normalize to depth of coverage across mitochondrial genome target?

#72 tessleuthner closed 3 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 2 years 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