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26 Open 52 Closed
26 Open 52 Closed
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Issues list

Negative mean coverage returned by dnmtools pmd
#255 opened Dec 30, 2024 by zhoujt1994
1
The hmr command fails when methylation levels are at extremes bug Something isn't working
#251 opened Nov 17, 2024 by andrewdavidsmith
Are there any parameters that need to be tuned for mapping WGBS data to repeat regions?
#248 opened Oct 23, 2024 by QianhuiWan
8
roi should check for input files before reporting any problems with arguments good first issue Good for newcomers
#154 opened Sep 30, 2023 by andrewdavidsmith
Keep non-CpG sites after sym command
#139 opened Sep 15, 2023 by natliang
mlml "error: chrom or pos mismatch in both files"
#135 opened Sep 12, 2023 by christianwake
3
selectsites failing with poor message on unsorted sites processed on disk
#123 opened Aug 31, 2023 by andrewdavidsmith
Comparison with other tools
#115 opened Aug 22, 2023 by moqri
Targeted Methylation Sequencing
#114 opened Aug 22, 2023 by moqri
amrfinder output
#71 opened Jul 18, 2023 by maggietsui
8
hmr requires symmetric data, fails on lifted over .meth files
#43 opened Jun 17, 2023 by faulk-lab
5
SYM - collapsing counts for other methylation context enhancement New feature or request
#41 opened May 11, 2023 by olaraym
2
radmeth-adjust replaces significant p-values in scientific notation with '1' and thus hides best DMC
#31 opened Feb 17, 2023 by iromeo
6
bigWig_to_methcounts
#28 opened Nov 4, 2022 by moqri
sensible output from levels command when run on symmetric CpG counts files question Further information is requested
#27 opened Nov 2, 2022 by andrewdavidsmith
space between AMRs for merging
#2 opened Jul 17, 2022 by andrewdavidsmith
roimethstat and order of chromosomes
#8 opened Jul 8, 2022 by andrewdavidsmith
2
radmeth is too slow
#19 opened Jul 8, 2022 by guilhermesena1
HMRs for replicates should be able to read tabular format enhancement New feature or request
#9 opened Jul 7, 2022 by andrewdavidsmith
radmeth adjust outputs -1-1 in 7th field
#10 opened Jul 7, 2022 by guilhermesena1
Update PMD documentation to specify expected array input
#20 opened Jul 5, 2022 by guilhermesena1
Methcounts format for array data
#23 opened Jun 24, 2022 by andrewdavidsmith
the entropy values of all CpG sites were negative
#15 opened Jan 26, 2022 by vanessayang0927
1
roimethstat seems not be able to identify overlapping region
#21 opened Jan 24, 2022 by kyliuae
5
Radmeth Merge DMR Criterion question Further information is requested
#13 opened Feb 12, 2020 by SDeans0
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