geronimp/enrichM issues and pull requests

#137 - keyERROR

Issue - State: open - Opened by mengyuan09876 about 1 year ago - 1 comment

#136 - Issues with Conda installation

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

#135 - K00362 cannot assign to model M00530

Issue - State: closed - Opened by qikongwanli over 2 years ago

#134 - feat(BPA-628): added a boolean for checking ENRICMDB

Pull Request - State: closed - Opened by areejalsheikh over 2 years ago - 1 comment

#133 - feat(BPA-627): prints None when there are not hits

Pull Request - State: closed - Opened by areejalsheikh over 2 years ago

#132 - Error receiving while generating database

Issue - State: open - Opened by jayramr over 2 years ago

#131 - Update data.py

Pull Request - State: open - Opened by abhijeetsingh1704 about 3 years ago

#130 - Missing KO in my ko_frequency_table.tsv

Issue - State: open - Opened by PSSchacksen over 3 years ago

#129 - udpates

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

#128 - Dev/add doco

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

#127 - issues with help page/wiki

Issue - State: open - Opened by JinjinyuCityu over 3 years ago

#126 - AttributeError: 'Databases' object has no attribute 'M2DEF'

Issue - State: closed - Opened by wdp9966 almost 4 years ago - 1 comment

#125 - enrichM database

Issue - State: open - Opened by fanlu-f almost 4 years ago - 5 comments

#124 - minor bugfixes

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

#123 - fuzzywuzzi missing from conda env

Issue - State: open - Opened by wwood almost 4 years ago - 1 comment

#122 - README.md: Update conda install instructions.

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

#121 - enrichm annotate KO frequency table but all zeros

Issue - State: open - Opened by mhyleung almost 4 years ago - 3 comments

#120 - Index out of range error during enrichm annotate

Issue - State: closed - Opened by mhyleung almost 4 years ago - 2 comments

#119 - enrichm error

Issue - State: open - Opened by jianshu93 about 4 years ago

#118 - Dev/0.6.2.at2

Pull Request - State: closed - Opened by geronimp about 4 years ago

#117 - download the database separately

Issue - State: closed - Opened by liupfskygre about 4 years ago - 2 comments

#116 - ERROR while classifying using custom module

Issue - State: closed - Opened by ShailNair about 4 years ago - 2 comments

#115 - cannot open help pages/wiki

Issue - State: open - Opened by Caelyn996 about 4 years ago - 1 comment

#114 - 0.5.1 run error

Issue - State: open - Opened by jianshu93 over 4 years ago - 2 comments

#113 - fix #112

Pull Request - State: closed - Opened by SilasK over 4 years ago - 2 comments

#112 - There is probably a wrong version of urlib in the conda package.

Issue - State: closed - Opened by SilasK over 4 years ago

#111 - bioconda package

Issue - State: closed - Opened by SilasK over 4 years ago

#110 - "xargs: illegal option -- -" leading to "No files found with .faa suffix in input directory"

Issue - State: closed - Opened by SvenTobias-Hunefeldt over 4 years ago

#109 - Custom Database

Issue - State: open - Opened by Abonacolta over 4 years ago

#108 - Error opening file /home/databases/enrichm_database_v10/databases/uniref100.dmnd

Issue - State: open - Opened by zyyalice over 4 years ago - 1 comment

#107 - Bug fix and new features

Pull Request - State: closed - Opened by apcamargo over 4 years ago - 2 comments

#106 - Scripts to update the database

Issue - State: closed - Opened by apcamargo over 4 years ago - 7 comments

#105 - write splits characters in module path header

Issue - State: closed - Opened by minillinim over 4 years ago - 1 comment

#104 - enrichm classify fails on blank lines in input file

Issue - State: closed - Opened by minillinim over 4 years ago

#103 - Database downloader is not working

Issue - State: closed - Opened by apcamargo over 4 years ago - 3 comments

#102 - Pathway-cytoscape

Issue - State: open - Opened by Taojianchang almost 5 years ago

#101 - AttributeError: 'Databases' object has no attribute 'REF_DIR'

Issue - State: open - Opened by Thexiyang almost 5 years ago - 8 comments
Labels: bug

#100 - enrichm enrichment error

Issue - State: open - Opened by Taojianchang almost 5 years ago - 4 comments
Labels: bug

#99 - Issues installing/referencing the database

Issue - State: open - Opened by waoverholt almost 5 years ago - 3 comments

#98 - Enrichment - PCA plots and KO breakdown plots not generated

Issue - State: open - Opened by ashley-isaac about 5 years ago - 3 comments

#97 - Update databases

Pull Request - State: closed - Opened by wwood about 5 years ago

#96 - Nucleotide sequences of genes in 'genome_genes' directory all have identical sequences

Issue - State: open - Opened by rhysnewell about 5 years ago - 3 comments
Labels: bug

#95 - What does --depth in enricm explore mean?

Issue - State: open - Opened by TYMichaelsen about 5 years ago - 2 comments
Labels: question

#94 - Error: ln: missing file operand when running 'enrichm annotate'

Issue - State: closed - Opened by signalbash about 5 years ago - 3 comments

#93 - Using custom databases for annotation

Issue - State: open - Opened by adityabandla about 5 years ago - 4 comments

#92 - Error when using protein sequences

Issue - State: open - Opened by ashley-isaac about 5 years ago - 2 comments
Labels: enhancement

#91 - gene naming issue

Issue - State: open - Opened by wwood over 5 years ago - 1 comment
Labels: bug

#90 - toolbox: Use subprocess.check_call not call

Pull Request - State: closed - Opened by wwood over 5 years ago

#89 - Incorrect database file name

Issue - State: open - Opened by liangjinsong over 5 years ago - 6 comments
Labels: bug

#88 - Error when downloading database

Issue - State: closed - Opened by liangjinsong over 5 years ago - 1 comment

#87 - Cannot install using conda

Issue - State: open - Opened by hkoo877 over 5 years ago - 2 comments

#86 - ZeroDivisionError in annotate

Issue - State: open - Opened by ganiatgithub over 5 years ago - 3 comments

#85 - Geronimp cleanup of annotate

Pull Request - State: closed - Opened by geronimp over 5 years ago

#84 - GFF generating failure when supplying own proteomes

Issue - State: closed - Opened by wwood over 5 years ago - 3 comments

#83 - annotate: Soft link rather than copy input genomes.

Pull Request - State: closed - Opened by wwood over 5 years ago - 2 comments

#82 - Large disk usage for lotsa genomes input

Issue - State: closed - Opened by wwood over 5 years ago - 1 comment

#81 - super long run time for 2 genomes

Issue - State: open - Opened by ganiatgithub over 5 years ago - 4 comments

#80 - classify error : ZeroDivisionError: division by zero

Issue - State: closed - Opened by michoug over 5 years ago - 1 comment
Labels: bug

#79 - enrichm annotate fasta file error

Issue - State: closed - Opened by TYMichaelsen over 5 years ago - 2 comments
Labels: bug

#78 - --custom_modules not working

Issue - State: closed - Opened by TYMichaelsen over 5 years ago - 3 comments

#77 - help page/wiki

Issue - State: closed - Opened by ganiatgithub over 5 years ago - 4 comments

#76 - Missing ko_cutoffs.tsv in the database

Issue - State: closed - Opened by michoug over 5 years ago - 3 comments

#75 - Linting and tests

Pull Request - State: closed - Opened by geronimp over 5 years ago

#74 - Directionality on reactions for enrichm pathway/explore?

Issue - State: closed - Opened by TYMichaelsen over 5 years ago - 2 comments
Labels: enhancement

#73 - Refactoring

Pull Request - State: closed - Opened by geronimp over 5 years ago

#72 - Make --metadata optional in enrichm pathway/explore?

Issue - State: closed - Opened by TYMichaelsen over 5 years ago - 3 comments
Labels: enhancement

#71 - custom modules for metacyc

Pull Request - State: closed - Opened by geronimp over 5 years ago

#70 - enrichm explore AttributeError

Issue - State: closed - Opened by TYMichaelsen over 5 years ago - 7 comments
Labels: bug

#69 - dump

Pull Request - State: closed - Opened by geronimp over 5 years ago

#68 - nucleotide introduced, new flags

Pull Request - State: closed - Opened by geronimp almost 6 years ago

#67 - Code cleanup

Pull Request - State: closed - Opened by geronimp almost 6 years ago

#66 - Classify bugs

Pull Request - State: closed - Opened by geronimp almost 6 years ago

#65 - Kohmm cutoffs

Pull Request - State: closed - Opened by geronimp almost 6 years ago

#64 - Module problems

Pull Request - State: closed - Opened by geronimp almost 6 years ago

#63 - Ben bug

Pull Request - State: closed - Opened by geronimp almost 6 years ago

#62 - bin: Adjust an author name.

Pull Request - State: closed - Opened by wwood almost 6 years ago - 1 comment

#61 - Add ko hmm annotation pipeline

Pull Request - State: closed - Opened by geronimp almost 6 years ago