Issues

• Crashes when chromosomes have no CpG sites

  smithlabcode/dnmtools#307 · Filter by author andrewdavidsmith opened on Nov 12, 2025

• the interpretation of the amrfinder output

  smithlabcode/dnmtools#297 · Filter by author JJJelly77 opened on Sep 23, 2025

• Blank output from dnmtools amrfinder

  smithlabcode/dnmtools#296 · Filter by author JJJelly77 opened on Sep 23, 2025

• Merge and dnmtools hmr-rep

  smithlabcode/dnmtools#291 · Filter by author vagan21 opened on Aug 29, 2025
  1

• SAM file is not sorted ERROR even if the input file is sorted

  smithlabcode/dnmtools#260 · Filter by author YuanfengZhang opened on May 12, 2025
  5

• regions not sorted in file

  smithlabcode/dnmtools#257 · Filter by author JavenCao opened on Feb 14, 2025
  4

• Negative mean coverage returned by dnmtools pmd

  smithlabcode/dnmtools#255 · Filter by author zhoujt1994 opened on Dec 30, 2024
  1

• The hmr command fails when methylation levels are at extremes

  bug
  smithlabcode/dnmtools#251 · Filter by author andrewdavidsmith opened on Nov 17, 2024

• Are there any parameters that need to be tuned for mapping WGBS data to repeat regions?

  smithlabcode/dnmtools#248 · Filter by author QianhuiWan opened on Oct 23, 2024
  8

• roi should check for input files before reporting any problems with arguments

  good first issue
  smithlabcode/dnmtools#154 · Filter by author andrewdavidsmith opened on Sep 30, 2023

• Keep non-CpG sites after sym command

  smithlabcode/dnmtools#139 · Filter by author natliang opened on Sep 15, 2023

• mlml "error: chrom or pos mismatch in both files"

  smithlabcode/dnmtools#135 · Filter by author christianwake opened on Sep 12, 2023
  3

• selectsites failing with poor message on unsorted sites processed on disk

  smithlabcode/dnmtools#123 · Filter by author andrewdavidsmith opened on Aug 31, 2023

• Comparison with other tools

  smithlabcode/dnmtools#115 · Filter by author moqri opened on Aug 22, 2023

• Targeted Methylation Sequencing

  smithlabcode/dnmtools#114 · Filter by author moqri opened on Aug 22, 2023

• amrfinder output

  smithlabcode/dnmtools#71 · Filter by author maggietsui opened on Jul 18, 2023
  8

• hmr requires symmetric data, fails on lifted over .meth files

  smithlabcode/dnmtools#43 · Filter by author faulk-lab opened on Jun 17, 2023
  5

• SYM - collapsing counts for other methylation context

  enhancement
  smithlabcode/dnmtools#41 · Filter by author olaraym opened on May 11, 2023
  2

• radmeth-adjust replaces significant p-values in scientific notation with '1' and thus hides best DMC

  smithlabcode/dnmtools#31 · Filter by author iromeo opened on Feb 17, 2023
  6

• bigWig_to_methcounts

  smithlabcode/dnmtools#28 · Filter by author moqri opened on Nov 4, 2022

• sensible output from levels command when run on symmetric CpG counts files

  question
  smithlabcode/dnmtools#27 · Filter by author andrewdavidsmith opened on Nov 2, 2022

• space between AMRs for merging

  smithlabcode/dnmtools#2 · Filter by author andrewdavidsmith opened on Jul 17, 2022

• roimethstat and order of chromosomes

  smithlabcode/dnmtools#8 · Filter by author andrewdavidsmith opened on Jul 8, 2022
  2

• HMRs for replicates should be able to read tabular format

  enhancement
  smithlabcode/dnmtools#9 · Filter by author andrewdavidsmith opened on Jul 7, 2022

• radmeth adjust outputs -1-1 in 7th field

  smithlabcode/dnmtools#10 · Filter by author guilhermesena1 opened on Jul 7, 2022