im3sanger/dndscv

Issues

• Genes missing in hg38 ref file

  #100 opened a month ago by sahilseth
  0

• How do I run Duplex sequence results with dndscv/

  #99 opened a month ago by zongdawu
  0

• calculation of dn/ds for bacterial genome data

  #98 opened 2 months ago by chantisakee
  2

• No genes with qglobal_cv < 0.1

  #69 opened 3 years ago by kvn95ss
  6

• Can we calculate dN/dS ratio for each sample?

  #97 opened 4 months ago by lincj1994
  1

• can mutations contains indels?

  #96 opened 5 months ago by complexgenome
  1

• using which refCDS-hg38? doubt for covariate

  #95 opened 5 months ago by complexgenome
  1

• Arguments imply differing number of rows

  #86 opened 2 years ago by parvathisudha
  9

• Error loading the hg38 reference database and the hg38 covariate files

  #94 opened 9 months ago by gat2010
  1

• dndsout = dndscv(df) output error messages

  #93 opened 9 months ago by HendrinaS
  1

• question about confidence interval for INDELs

  #91 opened a year ago by loipf
  3

• signif_genes = sel_cv[sel_cv$qglobal_cv<0.1, c("gene_name","qglobal_cv")] error

  #92 opened a year ago by HendrinaS
  1

• estimating global dNdSCV ratios from subsets of coding mutations

  #81 opened 2 years ago by bkinnersley
  2

• Zero values in some columns

  #90 opened 2 years ago by FL512
  1

• 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 opened 2 years ago by manchengyanyu
  0

• Build Ref error

  #59 opened 4 years ago by ggoodstudydaydayup
  1

• Is there a way to change the omega(w) values

  #87 opened 2 years ago by ykginoue
  5

• All the values of qglobal_cv are zero

  #68 opened 2 years ago by vivekruhela
  4

• Error when trying to use buildref() : Error in new_codon[1, ]: incorrect number of dimensions

  #85 opened 2 years ago by tly0505
  1

• qglobal_cv of the top genes were zero.

  #77 opened 2 years ago by lincj1994
  1

• How to verify the mutations are independent events?

  #84 opened 2 years ago by Sunsq1997
  1

• Could you add qind_cv to the output of sel_cv?

  #82 opened 2 years ago by njbernstein
  1

• Error in while ((it <- it + 1) < limit && abs(del) > eps)

  #83 opened 2 years ago by zhuhenan
  1

• The meaning of 'tml' in the 'dndscv.R'

  #80 opened 2 years ago by Sunsq1997
  0

• dNdS script takes a lot of time to run

  #79 opened 3 years ago by sakrnference
  4

• Apply dndscv to a Non-cancer population with high recombination

  #74 opened 3 years ago by huangl-CAU
  1

• 5-nucleotide context mutational signature

  #76 opened 3 years ago by andreyurch
  1

• Handling of DBS

  #78 opened 3 years ago by ishida-md
  1

• Error when installing dndsv using: install_github("im3sanger/dndscv")

  #75 opened 3 years ago by sakrnference
  6

• Normalize to depth of coverage across mitochondrial genome target?

  #72 opened 3 years ago by tessleuthner
  1

• issue about position of input file

  #73 opened 3 years ago by stroke1989
  1

• No qglobal_cv in "sel_cv"

  #71 opened 3 years ago by WangKang-Leo
  1

• Zero coding substitutions found in this dataset

  #60 opened 3 years ago by eoinmck
  4

• A wrong parameter in substmodel "192r_3w"?

  #70 opened 3 years ago by kakiuchi-kyt
  1

• Didn't get pglobal_cv and qglobal_cv columns in the output file from the 1st step

  #67 opened 3 years ago by RupalHatkar
  3

• Very high dnds values

  #66 opened 3 years ago by ArashDepp
  3

• Interpreting dndscv results

  #64 opened 3 years ago by loukesio
  7

• how to find genes with signature of purifying selection from dNdSCV results

  #63 opened 4 years ago by shaghayeghsoudi
  3

• How to use dndscv in bacteria species?

  #62 opened 4 years ago by loukesio
  7

• Fail to install

  #61 opened 4 years ago by missstcxq
  1

• Error in RefCDS[[j]] : subscript out of bounds

  #55 opened 4 years ago by CraigJAnderson
  2

• Name clash error on load

  #57 opened 4 years ago by luca-dex
  0

• qglobal_cv and qallsubs_cv = 1

  #56 opened 4 years ago by antu2817
  2

• Help troubleshooting metastasis analysis

  #54 opened 4 years ago by carladosanjos
  1

• Can you explain mrfold?

  #53 opened 4 years ago by njbernstein
  1

• Help troubleshooting global dn/ds

  #51 opened 4 years ago by njbernstein
  7

• Regarding Zero coding substitutions found in this dataset.

  #52 opened 4 years ago by SmritiChawla
  2

• columns qmis_cv, qtrunc_cv, qallsubs_cv, pglobal_cv, qglobal_cv NA

  #49 opened 4 years ago by guidmt
  1

• hg38 ref files

  #50 opened 4 years ago by alhafidzhamdan
  1

• Error in names(x) <- value : 'names' attribute [10] must be the same length as the vector [9]

  #48 opened 4 years ago by carladosanjos
  2