Ecosyste.ms: Issues

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GitHub / chg60/DEPhT issues and pull requests

#50 - about download database ande train model

Issue - State: open - Opened by swayintheair about 1 month ago

#49 - Update LICENSE

Pull Request - State: open - Opened by chg60 about 2 months ago

#48 - Is it suitable for metagenome-assembled genomes (MAGs)?

Issue - State: closed - Opened by WoCer2019 4 months ago - 2 comments

#47 - HTML Output Issue

Issue - State: open - Opened by bbshockey 11 months ago - 3 comments

#46 - Strand must be passed to FeatureLocation now

Pull Request - State: closed - Opened by peterjc about 1 year ago

#45 - Problems running DEPhT

Issue - State: closed - Opened by ntmscope about 1 year ago - 10 comments

#44 - Issues Encountered During Model Training

Issue - State: open - Opened by zequanhan about 1 year ago - 4 comments

#43 - Specific model for Providencia and Klebsiella pneumoniae phages

Issue - State: open - Opened by Dx-wmc over 1 year ago - 2 comments

#42 - Installation of DEPht

Issue - State: closed - Opened by aamaniii0 over 1 year ago - 2 comments

#41 - Missing releases and tags

Issue - State: closed - Opened by SethosII over 1 year ago

#40 - Arthrobacter model?

Issue - State: closed - Opened by edgingtonn1 over 1 year ago - 5 comments
Labels: enhancement

#39 - accept as input gzipped fasta

Issue - State: open - Opened by igortru about 2 years ago - 2 comments
Labels: enhancement

#38 - Problems with model training

Issue - State: closed - Opened by gaworj over 2 years ago - 10 comments

#37 - There is no .html file in result

Issue - State: closed - Opened by Mr-Wornock over 2 years ago - 3 comments

#36 - Removed networkx dependancy; reweighted ref blast; slightly lowered …

Pull Request - State: closed - Opened by chg60 over 3 years ago

#35 - Refdb dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#34 - Depht utils dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#33 - Depht utils dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#32 - Added minimum probability threshold filter onto prophage regions dete…

Pull Request - State: closed - Opened by chg60 over 3 years ago

#31 - better_boundaries_dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#30 - Added core family bacterial markings in mmseqs subpipeline

Pull Request - State: closed - Opened by chg60 over 3 years ago

#29 - Added/removed genomes from protein product fasta database

Pull Request - State: closed - Opened by chg60 over 3 years ago

#28 - Dump option now acts to dump bacterial data regardless of prophage co…

Pull Request - State: closed - Opened by chg60 over 3 years ago

#27 - Att dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#26 - Fixed bugs pertaining to fast mode, lack of att sites

Pull Request - State: closed - Opened by chg60 over 3 years ago

#25 - Att dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#24 - Contig dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#23 - Cleaned up mmseqs temp output

Pull Request - State: closed - Opened by chg60 over 3 years ago

#22 - Modified integrase distance scoring function; changed hhsearch databa…

Pull Request - State: closed - Opened by chg60 over 3 years ago

#21 - UI dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#20 - Replaced context managed filehandles with explicit open() and close()…

Pull Request - State: closed - Opened by chg60 over 3 years ago

#19 - Merge dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#18 - Mmseqs dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#17 - Att dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#16 - Gui dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#15 - Testing dev

Pull Request - State: closed - Opened by chg60 over 3 years ago

#14 - Docs dev

Pull Request - State: closed - Opened by laa89 almost 4 years ago

#13 - Docs dev

Pull Request - State: closed - Opened by laa89 almost 4 years ago

#12 - Att dev

Pull Request - State: closed - Opened by chg60 almost 4 years ago

#11 - Compiled naive pipeline

Pull Request - State: closed - Opened by chg60 almost 4 years ago

#10 - benchmarking code

Pull Request - State: closed - Opened by chg60 almost 4 years ago

#9 - Added __main__.py runscript

Pull Request - State: closed - Opened by chg60 almost 4 years ago

#8 - Hhsearch dev

Pull Request - State: closed - Opened by chg60 almost 4 years ago

#7 - Revamped and restored bloom filter/DeBruijn graph att site algorithm

Pull Request - State: closed - Opened by chg60 almost 4 years ago

#6 - added wrapper function module

Pull Request - State: closed - Opened by chg60 almost 4 years ago

#5 - Stitch dev

Pull Request - State: closed - Opened by chg60 almost 4 years ago

#4 - Removed capitol P prophicient module root directory

Pull Request - State: closed - Opened by chg60 almost 4 years ago

#3 - Att dev

Pull Request - State: closed - Opened by chg60 almost 4 years ago

#2 - Att dev

Pull Request - State: closed - Opened by chg60 almost 4 years ago

#1 - merge utilities_dev

Pull Request - State: closed - Opened by chg60 almost 4 years ago