Recent Releases of dovip_lib.jl
dovip_lib.jl -
fixed issues with calculate initial predictors coverage
- Julia
Published by CristinaMoraru 8 months ago
dovip_lib.jl -
fixed bug in group proviruses, merge_prophages()
- Julia
Published by CristinaMoraru 10 months ago
dovip_lib.jl -
updated code for genomad v1.11 and dependencies
- Julia
Published by CristinaMoraru 10 months ago
dovip_lib.jl -
- Added functionality to unMix viruses found both on the integrated and non-integrated branch
- Added a geNomad taxonomy step to classify all viral contigs
- replaced the sum of all predictors with "initial predictor coverage"
- some other small fixes
- Julia
Published by CristinaMoraru 10 months ago
dovip_lib.jl -
Major updates in the DoViP_Lib:
- added functionality to resolve the mixed viral contigs (found in both the integrated and non-integrated branches)
- added a step to calculate taxonomy with geNomad for all viral fragments from all initial predictors (as opposed to having the - taxonomy only for those fragments predicted by geNomad)
- added functionality to calculate for viral sequences on the integrated branch the "predictor coverage" and to use it for the - final thresholding step
- updated folder names
- fixed some other minor issues
- - used for testing on the Isol dataset
- Julia
Published by CristinaMoraru 10 months ago
dovip_lib.jl -
Major updates in the DoViP_Lib: - added functionality to resolve the mixed viral contigs (found in both the integrated and non-integrated branches) - added a step to calculate taxonomy with geNomad for all viral fragments from all initial predictors (as opposed to having the taxonomy only for those fragments predicted by geNomad) - added functionality to calculate for viral sequences on the integrated branch the "predictor coverage" and to use it for the final thresholding step - updated folder names - fixed some other minor issues
- Julia
Published by CristinaMoraru 10 months ago
dovip_lib.jl -
Changes to the run-workflow functions to accomodate further cases when no virus contigs are detected by the initial virus predictors, or where removed from by DoViP during the post-processign filtering steps
- Julia
Published by CristinaMoraru over 1 year ago
dovip_lib.jl -
changes to the merge_nonintegrated and a few other functions to accomodate further cases when no virus contigs are detected by the initial virus predictors, or where removed from by DoiP during the post-processign filtering steps
- Julia
Published by CristinaMoraru over 1 year ago
dovip_lib.jl -
- changes to the exportaggregatedint function to accomodate the case when one contig is detected as circular by VirSorter, but not by DoViP
- updated versiond of BioSExtTools.jl (v0.4.2) and BioSSeqFuns.jl (v0.2.3)
- Julia
Published by CristinaMoraru over 1 year ago
dovip_lib.jl -
Updated the Project.toml and Manifest.toml files
- Julia
Published by CristinaMoraru over 1 year ago
dovip_lib.jl -
- major code changes (e.g. changed function for calculation of contig shaoe and ends, and when in the workflow is beeing calculated; changed automatic trimming of DTR from the contig ends, in the new version both trimmed and untrimmed sequences are given; added further conditions for final thresholding, which account for checkV circular contigs)
- the dependency BioSSeqFuns was added with add https://github.com/CristinaMoraru/BioSSeqFuns.jl#v0.2.2
- Julia
Published by CristinaMoraru over 1 year ago
dovip_lib.jl - v0.8.1
Minor updates
Full Changelog: https://github.com/CristinaMoraru/DoViP_Lib.jl/compare/v0.8.0...v0.8.1
- Julia
Published by CristinaMoraru over 1 year ago