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A deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads of plants

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bug fixes

enable .gz output in extract/call_mods/call_freq modules

multi-gpu support in call_mods module

update requirements/dependences


make sure results of each read be written together in call_mods’ output

make –reference_path not a required input in extract and call_mods module


modify call_freq module for large genomes,

fix bug of extrating contig name from fast5s


add ranger optimizer and modify train module,

fix Queue.qsize() NotImplementedError in macOS partially, however call_mods in CUDA mode in macOS still doesn’t work,

add init_model option in train module


change imports in ref_reader,

change requirements,

fix and modify denoise module,

fix MKL_THREADING_LAYER error temporarily,

add –region option,

a combined 5mC model replacing CG/CHG/CHH models


fix bug and optimize call_mods without GPU, add call_freq funciton


Release the first vesrion of deepsignal-plant package

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deepsignal-plant-0.1.6.tar.gz (55.3 kB view hashes)

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