Code

clean/reports#189

Code

Merged

alexg9010 merged 20 commits intomainBIMSBbioinfo/pigx_bsseq:mainfrom clean/reportsBIMSBbioinfo/pigx_bsseq:clean/reportsCopy head branch name to clipboardJul 19, 2024

+235-292

Commits

Commits on Jul 19, 2024

• index.Rmd.in: move global flags out of params

  Show description for 796f13c
  alexg9010

  committed
  796f13c

• index.Rmd.in: load libraries early on

  Show description for c52b8bb
  alexg9010

  committed
  c52b8bb

• index.Rmd.in: fix error in annotateWithGeneParts

  Show description for 35beacd
  alexg9010

  committed
  35beacd

• fix ggplot function overwrite caused by ideoDMC.r

  Show description for a2c60b9
  alexg9010

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  a2c60b9

• diffmeth.Rmd: change order of check logic

  Show description for 79ba22b
  alexg9010

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  79ba22b

• diffmeth.rmd: split chunks

  Show description for be77946
  alexg9010

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  be77946

• diffmeth.rmd: split chunks

  Show description for 74feb5a
  alexg9010

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  74feb5a

• diffmeth.rmd: fix formatting issues

  Show description for c125d7a
  alexg9010

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  c125d7a

• generate_report: fix printing of wrong argument

  Show description for c407b4d
  alexg9010

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  c407b4d

• generate_report: improve printing and export of given arguments

  Show description for 4520c06
  alexg9010

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  4520c06

• generate_report: apply formatter

  Show description for cdcbc73
  alexg9010

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  cdcbc73

• accept refGene annotation file

  alexg9010

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  51e760b

• omit web fetching for annotation files

  Show description for db01210
  alexg9010

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  db01210

• remove webfetch from diffmeth report

  alexg9010

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  741339f

• omit web fetching for sample reports

  Show description for df5053c
  alexg9010

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  df5053c

• update sample report

  Show description for 5a7823b
  alexg9010

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  5a7823b

• move annotation files to location section of settings

  alexg9010

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  e61e75d

• update validation

  Show description for 6a7a819
  alexg9010

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  6a7a819

• add mark to indicate optional arguments

  alexg9010

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  842086a

• remove annotation dict from test settings

  alexg9010

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  a4a48be