Issues

• How to empirically determine, from my own dataset, which option performs best for hi.perc, overdispersion, adjust, and win.size/step.size

  al2na/methylKit#373 · Filter by author ligia-26 opened on Sep 16, 2026
  2

• methylKit 1.33.3 (bioconductor version 1.38.0) fails to compile with GCC 15 / C++20: const char* to char* conversion in methCall.cpp

  al2na/methylKit#371 · Filter by author brianlamere opened on Sep 12, 2026
  1

• inconsistent calculateDiffMeth results when re-ordering methylBase columns and swapping treatment 0/1 annotations

  al2na/methylKit#370 · Filter by author hd2326 opened on Aug 28, 2026
  2

• When have more than one experimental group, how to assign

  al2na/methylKit#366 · Filter by author ajneville opened on Oct 16, 2025
  2

• add check if methylKit::unite with min.per.group filter would work for given sample number and chunk size

  al2na/methylKit#363 · Filter by author alexg9010 opened on Aug 12, 2025

• Unite() function in methylkit shows error when destrand = TRUE

  al2na/methylKit#362 · Filter by author ChandanaRao4 opened on Jul 31, 2025
  3

• Error in if (length(df) == 7 & unique(sapply(df, class)[5:7]) == "integer") { : the condition has length > 1

  enhancement
  al2na/methylKit#360 · Filter by author HuangRuocheng opened on Jun 5, 2025
  2

• wrong output file path is checked for existence

  enhancement
  al2na/methylKit#358 · Filter by author alexg9010 opened on Apr 16, 2025
  

• prevent doubling of DT:tabix in tabix header

  al2na/methylKit#357 · Filter by author alexg9010 opened on Apr 10, 2025
  

• Allow specifying DB files directly

  al2na/methylKit#355 · Filter by author J-Moravec opened on Apr 4, 2025
  1

• Doubling suffixes in calculateDiffMeth

  document
  al2na/methylKit#353 · Filter by author J-Moravec opened on Apr 3, 2025
  4

  

• assembly cannot be empty string '""'

  bug
  al2na/methylKit#352 · Filter by author J-Moravec opened on Apr 3, 2025
  1

  

• Error in unite() when specifying destrand = TRUE

  al2na/methylKit#349 · Filter by author BenTPTseng opened on Mar 10, 2025
  2

• tileMethylCounts Execution halted

  al2na/methylKit#337 · Filter by author yhj-j opened on Jan 10, 2025
  1

• Extract the most differentially methylated genes

  al2na/methylKit#328 · Filter by author AlbanZimmer opened on Sep 20, 2024

• Issue in unite funtion

  al2na/methylKit#326 · Filter by author Anjaligarg006 opened on Aug 27, 2024
  7

• how to use the methylation data when to do boxplot ?

  al2na/methylKit#324 · Filter by author Xiangyi-Deng opened on Aug 8, 2024
  4

• NA values

  al2na/methylKit#323 · Filter by author Silvia-Giorgia-Signorini opened on Jul 9, 2024
  1

• Support for all context all types of methylation data

  al2na/methylKit#322 · Filter by author Ge0rges opened on May 22, 2024

• Typo in vignette

  al2na/methylKit#312 · Filter by author llrs opened on Jan 30, 2024

• Error reading in file

  improve error message
  al2na/methylKit#302 · Filter by author Ge0rges opened on Oct 8, 2023
  3

  

• methylKit "unite" function error message

  al2na/methylKit#296 · Filter by author mirurb opened on Aug 18, 2023
  5

  

• add 'chunk' option for getData

  document
  al2na/methylKit#292 · Filter by author RJDan opened on Jul 14, 2023
  2

  

• Error during methylkit unite

  bug
  al2na/methylKit#290 · Filter by author manjumoorthy95 opened on Jul 10, 2023
  1

  

• check for duplicated regions in regioncounts

  al2na/methylKit#288 · Filter by author alexg9010 opened on Jun 23, 2023