Skip to main content

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

Project description

Release

0.1.6

bug fixes

enable .gz output in extract/call_mods/call_freq modules

multi-gpu support in call_mods module

update requirements/dependences

0.1.5

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

0.1.4

modify call_freq module for large genomes,

fix bug of extrating contig name from fast5s

0.1.3

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

0.1.2

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

0.1.1

fix bug and optimize call_mods without GPU, add call_freq funciton

0.1.0

Release the first vesrion of deepsignal-plant package

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

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

Uploaded Source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page