Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / bionf/phyloprofile issues and pull requests

#130 - Update README.md

Pull Request - State: closed - Opened by trvinh 24 days ago

#129 - Speed up parsing new taxa

Issue - State: open - Opened by trvinh 7 months ago
Labels: enhancement

#128 - Gene categories are plotted arbitrarily...

Issue - State: closed - Opened by bheimbu 8 months ago - 11 comments

#127 - Display different strains/isolates that have the same taxon ID

Issue - State: open - Opened by trvinh about 1 year ago
Labels: feature-request

#126 - Bugs in highlighting of main plot and updating customised plot

Issue - State: closed - Opened by trvinh over 1 year ago
Labels: bug

#125 - Option to update old taxon IDs for user input

Issue - State: open - Opened by trvinh almost 2 years ago
Labels: feature-request

#124 - option to use user defined taxonomy database

Issue - State: closed - Opened by trvinh almost 2 years ago
Labels: enhancement, feature-request

#123 - pre-generate taxonomy tree

Issue - State: closed - Opened by trvinh over 2 years ago
Labels: enhancement

#122 - input list of genes not works

Issue - State: closed - Opened by trvinh over 2 years ago
Labels: bug

#121 - Domain plot for the whole profile of a selected gene

Issue - State: open - Opened by trvinh almost 3 years ago
Labels: feature-request

#120 - EXTEND the function for exporting plot settings

Issue - State: open - Opened by trvinh almost 3 years ago
Labels: feature-request

#119 - User defined tree

Issue - State: closed - Opened by Yruegas almost 3 years ago - 1 comment

#118 - Option to download current taxonomy data OR import old tax data

Issue - State: closed - Opened by trvinh almost 3 years ago - 1 comment
Labels: feature-request

#117 - external links not work with non-fdog-format protein ID

Issue - State: closed - Opened by trvinh over 3 years ago

#116 - X Axis labels horizontal adjustment

Issue - State: closed - Opened by dominikper over 3 years ago - 1 comment

#115 - missing taxa when download customized profile - is it ok?

Issue - State: open - Opened by trvinh over 3 years ago
Labels: question

#114 - OMA Standalone OrthoXML error

Issue - State: closed - Opened by akiselev-lrsv almost 4 years ago - 6 comments

#112 - improve documentation

Issue - State: open - Opened by trvinh over 4 years ago
Labels: enhancement

#111 - convergence point

Issue - State: open - Opened by trvinh over 4 years ago
Labels: feature-request

#110 - plot features

Issue - State: closed - Opened by trvinh over 4 years ago
Labels: enhancement, feature-request

#109 - improve input / output options

Issue - State: open - Opened by trvinh over 4 years ago
Labels: enhancement, feature-request

#108 - Improve phylostratigraphy

Pull Request - State: closed - Opened by trvinh over 4 years ago

#107 - Improve rank indexing function

Pull Request - State: closed - Opened by trvinh over 4 years ago

#106 - converted dataframe into data.table obj for dcast and melt

Pull Request - State: closed - Opened by trvinh over 4 years ago

#105 - speed up PhyloProfile

Issue - State: open - Opened by trvinh about 5 years ago - 1 comment
Labels: enhancement

#104 - Bioc revision2 - cont. (function lengths 2)

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

#103 - Bioc revision2 - cont. (function lengths)

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

#102 - Bioc revision2 - cont.

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

#101 - Bioc revision2 - reduced dependency list

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

#100 - second revision for bioconductor

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

#99 - first revision for bioconductor

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

#98 - Update DESCRIPTION

Pull Request - State: closed - Opened by ermali7 over 5 years ago - 3 comments

#97 - Fixed errors for 1st bioconductor build

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

#96 - rooting user input tree

Issue - State: closed - Opened by trvinh about 6 years ago
Labels: feature-request

#95 - packaging

Pull Request - State: closed - Opened by trvinh about 6 years ago

#94 - V0.3.2

Pull Request - State: closed - Opened by trvinh about 6 years ago - 9 comments

#93 - V0.3.2 beta clustering

Pull Request - State: closed - Opened by trvinh about 6 years ago

#92 - Clustering

Pull Request - State: closed - Opened by CarlaMoelbert about 6 years ago

#91 - color of domain plot

Issue - State: closed - Opened by trvinh about 6 years ago
Labels: enhancement

#90 - Deactivating Auto update plot is not working

Issue - State: closed - Opened by jamawoko about 6 years ago
Labels: bug

#89 - Filter for number of co-orthologs

Issue - State: closed - Opened by jamawoko about 6 years ago - 1 comment
Labels: feature-request

#88 - removed conflict between 2 cluster_profile scripts

Pull Request - State: closed - Opened by trvinh over 6 years ago

#87 - Modularizing

Pull Request - State: closed - Opened by trvinh over 6 years ago - 3 comments

#86 - Modularizing Group comparison

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#85 - Modularizing Group Comparison

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#84 - Revert "Modularizing Group Comparison"

Pull Request - State: closed - Opened by trvinh over 6 years ago

#83 - Modularizing Group Comparison

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#82 - Modularizing Group Comparison

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#81 - Revert "Adding the module for group comparison"

Pull Request - State: closed - Opened by trvinh over 6 years ago

#80 - Adding the module for group comparison

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#79 - Obtain ncbi taxonomy from local database

Issue - State: closed - Opened by trvinh over 6 years ago - 1 comment
Labels: enhancement, feature-request

#78 - Long format input to large for upload

Issue - State: closed - Opened by evolgenomology over 6 years ago - 4 comments

#77 - Catching when a id has no members

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#76 - Showing domain Plot with oma input

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#75 - Catches if there is an invalid id in the oma input

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#74 - Added missing rows to data frame from the main input

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#73 - Added missing rows in the data frame for the main input

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#72 - Fixed a problem with the download of the files generated form the oma browser

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago - 1 comment

#70 - Integrate into a 'Galaxy Interactive Environment'

Issue - State: closed - Opened by dfornika over 6 years ago - 14 comments
Labels: enhancement, mozsprint

#69 - Added a list of OMA or Uniprot ids as input type

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#68 - Modularising app code

Issue - State: closed - Opened by trvinh over 6 years ago - 1 comment
Labels: enhancement, mozsprint

#67 - All functions are now in the functions Skript

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago - 1 comment

#66 - Bug: Could not find file server.R to run

Issue - State: closed - Opened by hnguyen411 over 6 years ago
Labels: bug, mozsprint

#65 - rewrite ncbiTaxonomyParser.pl using python

Issue - State: closed - Opened by trvinh over 6 years ago
Labels: enhancement, mozsprint

#64 - Comments on branch `v0.3.0-beta`

Issue - State: closed - Opened by ha0ye over 6 years ago - 2 comments
Labels: mozsprint, feature-request

#63 - Reconfigure as a package?

Issue - State: closed - Opened by ha0ye over 6 years ago - 2 comments
Labels: mozsprint, feature-request

#62 - issue with checkNewick function

Issue - State: closed - Opened by trvinh over 6 years ago - 2 comments
Labels: bug

#60 - write tests for new functions

Issue - State: closed - Opened by trvinh over 6 years ago - 2 comments
Labels: enhancement, mozsprint

#59 - check the correct format for domain input files

Issue - State: closed - Opened by trvinh over 6 years ago - 1 comment
Labels: enhancement, mozsprint

#58 - check the user-defined taxonomy file before processing

Issue - State: closed - Opened by trvinh over 6 years ago
Labels: enhancement, mozsprint

#57 - Small changes in the group comparison function

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago - 1 comment

#56 - improve the source code

Issue - State: closed - Opened by trvinh over 6 years ago - 3 comments
Labels: enhancement, mozsprint

#55 - wrong information for clicked point

Issue - State: closed - Opened by trvinh over 6 years ago
Labels: bug

#54 - new features for Group comparison

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#53 - Revert "Group comparison: Last changes on the Group-Comparison function"

Pull Request - State: closed - Opened by trvinh over 6 years ago

#52 - Group comparison: Last changes on the Group-Comparison function

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#51 - Handling missing inputs with req(...)

Issue - State: closed - Opened by trvinh over 6 years ago
Labels: mozsprint

#50 - data filter using uploaded list of genes

Issue - State: closed - Opened by trvinh over 6 years ago - 1 comment
Labels: bug

#49 - 20000001 is not larger than the largest ncbi taxonomy ID anymore

Issue - State: closed - Opened by trvinh over 6 years ago
Labels: bug

#48 - Group comparison

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago - 2 comments

#47 - Group comparison

Pull Request - State: closed - Opened by CarlaMoelbert over 6 years ago

#46 - accepted new main input and domain files, modified UI

Pull Request - State: closed - Opened by trvinh almost 7 years ago - 1 comment

#45 - Update README.md

Pull Request - State: closed - Opened by gedankenstuecke about 7 years ago - 1 comment

#44 - Added GH community essentials

Pull Request - State: closed - Opened by gedankenstuecke about 7 years ago - 1 comment

#43 - Making a first release

Issue - State: closed - Opened by gedankenstuecke about 7 years ago - 2 comments

#42 - check validity of main input

Pull Request - State: closed - Opened by trvinh about 7 years ago

#41 - prettified the help

Pull Request - State: closed - Opened by gedankenstuecke about 7 years ago

#40 - Readme-Link

Issue - State: closed - Opened by gedankenstuecke about 7 years ago - 5 comments

#39 - added poster to README.md

Pull Request - State: closed - Opened by gedankenstuecke about 7 years ago - 4 comments

#38 - Oma files

Pull Request - State: closed - Opened by gedankenstuecke about 7 years ago

#37 - Update ui.R

Pull Request - State: closed - Opened by gedankenstuecke about 7 years ago

#36 - Update ui.R

Pull Request - State: closed - Opened by gedankenstuecke about 7 years ago

#35 - Update server.R

Pull Request - State: closed - Opened by gedankenstuecke about 7 years ago

#34 - Update README.md

Pull Request - State: closed - Opened by gedankenstuecke about 7 years ago

#33 - Using the GH Wiki-pages

Issue - State: closed - Opened by gedankenstuecke about 7 years ago - 1 comment

#32 - demo files for OMA Standalone OrthoXML-converter are gone.

Issue - State: closed - Opened by gedankenstuecke about 7 years ago - 3 comments

#31 - privileges gone through repo-transfer

Issue - State: closed - Opened by gedankenstuecke about 7 years ago - 3 comments

#30 - added howto for get_oma_hogs.py

Pull Request - State: closed - Opened by gedankenstuecke about 7 years ago - 1 comment