Ecosyste.ms: Issues

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

GitHub / pachterlab/gget issues and pull requests

#136 - Dev -> main

Pull Request - State: closed - Opened by lauraluebbert about 1 month ago

#135 - Updated inversion function and commented out test in gget_mutate

Pull Request - State: closed - Opened by josephrich98 about 1 month ago

#134 - Sync dev and main

Pull Request - State: closed - Opened by lauraluebbert about 1 month ago

#133 - Dev -> main

Pull Request - State: closed - Opened by lauraluebbert about 1 month ago

#132 - sync main and dev

Pull Request - State: closed - Opened by lauraluebbert about 1 month ago

#131 - Dev -> main

Pull Request - State: closed - Opened by lauraluebbert about 1 month ago

#130 - Cosmic dev -> main

Pull Request - State: closed - Opened by lauraluebbert about 1 month ago

#129 - Issue finding ensembl database for homo_sapiens release 112 37

Issue - State: closed - Opened by JackCurragh about 1 month ago - 3 comments

#128 - Create gget_mutate.py

Pull Request - State: closed - Opened by josephrich98 about 2 months ago

#127 - matching dev and main

Pull Request - State: closed - Opened by lauraluebbert 2 months ago

#126 - matching dev and main

Pull Request - State: closed - Opened by lauraluebbert 2 months ago

#125 - Dev -> Main: minor website updates

Pull Request - State: closed - Opened by lauraluebbert 2 months ago

#124 - Dataverse data access module

Pull Request - State: open - Opened by abearab 3 months ago - 3 comments

#123 - Fix Windows issue with gget setup elm

Pull Request - State: closed - Opened by lauraluebbert 5 months ago

#122 - Add " to Windows command

Pull Request - State: closed - Opened by mboffelli 5 months ago

#121 - Add module to depmap database

Issue - State: open - Opened by lauraluebbert 5 months ago - 1 comment
Labels: enhancement

#120 - Dev -> main

Pull Request - State: closed - Opened by lauraluebbert 5 months ago

#119 - Is it possible to get all ELM's using gget?

Issue - State: closed - Opened by Abhishaike 6 months ago - 4 comments
Labels: enhancement

#118 - Module to download MitoCarta3 database

Issue - State: open - Opened by lauraluebbert 6 months ago
Labels: enhancement

#117 - Add module to COSMIC database

Pull Request - State: closed - Opened by AubakirovArman 6 months ago - 1 comment

#116 - Update elm.md

Pull Request - State: closed - Opened by anhchi172 6 months ago

#115 - KeyError: 'Primary_Acc'

Issue - State: closed - Opened by CLZHANG96 7 months ago - 3 comments

#114 - Add module for reactome

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

#112 - Add module to COSMIC database

Issue - State: closed - Opened by lauraluebbert 8 months ago
Labels: enhancement

#111 - Fix bug in gget cellxgene

Pull Request - State: closed - Opened by lauraluebbert 8 months ago

#110 - gget.cellxgene TileDBError error when trying to return anndata

Issue - State: closed - Opened by rpeys 8 months ago - 4 comments

#109 - Dev -> main

Pull Request - State: closed - Opened by lauraluebbert 8 months ago

#108 - Elm -> dev

Pull Request - State: closed - Opened by lauraluebbert 8 months ago

#107 - gget seq encounters missing gene name from uniprot and throws type error

Issue - State: closed - Opened by rhngla 9 months ago - 2 comments

#106 - Feature proposal: KEGG PATHWAY image generation

Pull Request - State: closed - Opened by noriakis 9 months ago - 2 comments

#105 - Laura is the best

Pull Request - State: closed - Opened by victorg775 9 months ago

#104 - Multiple sequence alignment for multiple species

Issue - State: closed - Opened by mini374 9 months ago - 10 comments

#103 - Request addition of Open Targets API

Issue - State: open - Opened by lakigigar 9 months ago
Labels: enhancement

#102 - Replace deprecated df.applymap with df.map

Pull Request - State: closed - Opened by vecerkovakaterina 10 months ago

#100 - Rewrite gget BLAST to use BLAST+ instead of deprecated NCBI server

Issue - State: open - Opened by lauraluebbert 11 months ago
Labels: enhancement

#99 - Fix text errors Spanish translation of gget website

Pull Request - State: closed - Opened by victorg775 11 months ago

#98 - Spanish translation of gget website

Pull Request - State: closed - Opened by lauraluebbert 11 months ago

#97 - Dev

Pull Request - State: closed - Opened by anhchi172 11 months ago

#96 - gget search synonym and fixture updates

Pull Request - State: closed - Opened by anhchi172 11 months ago

#95 - gget search with synonyms

Pull Request - State: closed - Opened by anhchi172 11 months ago

#94 - Enrichr

Pull Request - State: closed - Opened by anhchi172 11 months ago

#93 - Enrichr add background

Pull Request - State: closed - Opened by anhchi172 11 months ago - 1 comment

#92 - Update unit tests for new ensembl release

Pull Request - State: closed - Opened by anhchi172 12 months ago - 1 comment

#91 - gget pdb error in python

Issue - State: closed - Opened by Paulie-ai 12 months ago - 3 comments
Labels: bug

#89 - Specify version in ensembl "search" module

Issue - State: closed - Opened by KleinSamuel about 1 year ago - 2 comments
Labels: enhancement

#88 - Dev

Pull Request - State: closed - Opened by anhchi172 about 1 year ago

#87 - Update documentation census version to 2023-08-15

Pull Request - State: closed - Opened by anhchi172 about 1 year ago

#86 - Update Fixtures

Pull Request - State: closed - Opened by anhchi172 about 1 year ago

#85 - Request addition of Eukaryotic Linear Motif database

Issue - State: closed - Opened by lakigigar about 1 year ago - 1 comment
Labels: enhancement

#83 - Update unittest fixtures

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

#81 - dev -> main

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

#79 - Dev

Pull Request - State: closed - Opened by anhchi172 about 1 year ago

#78 - cellxgene filter improvements

Issue - State: closed - Opened by atolopko-czi about 1 year ago - 1 comment
Labels: enhancement

#77 - Add ensembl plants to search

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

#76 - Create CODE_OF_CONDUCT.md

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

#75 - Add ensembl plants to search

Pull Request - State: closed - Opened by tdido about 1 year ago - 2 comments

#74 - Fix license classifier

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

#73 - GENCODE GTFs+FASTAs

Issue - State: open - Opened by Yenaled about 1 year ago
Labels: enhancement

#72 - Dev -> main

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

#71 - gget blast can not restrict by taxonomy

Issue - State: open - Opened by abearab about 1 year ago
Labels: enhancement

#70 - Download only exons sequence

Issue - State: closed - Opened by irinatu over 1 year ago - 1 comment
Labels: enhancement

#69 - Added verbosity argument

Pull Request - State: closed - Opened by anhchi172 over 1 year ago

#68 - Added verbosity argument

Pull Request - State: closed - Opened by anhchi172 over 1 year ago

#67 - dev -> main gget gpt with new API endpoint

Pull Request - State: closed - Opened by lauraluebbert over 1 year ago

#66 - Dev -> main gget gpt

Pull Request - State: closed - Opened by lauraluebbert over 1 year ago

#65 - Option to reduce verbosity or turn off logging

Issue - State: closed - Opened by gouinK over 1 year ago - 4 comments
Labels: enhancement

#64 - Dev

Pull Request - State: closed - Opened by lauraluebbert over 1 year ago

#63 - Speeding up gget.info by making pdb search mutable

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

#62 - Alphafold running time

Issue - State: closed - Opened by almart7 over 1 year ago - 4 comments

#61 - Change gget search url to useast Ensembl mirror

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

#60 - Improve 'curl is missing' error for gget ref -d (include link to install instructions)

Issue - State: closed - Opened by adamrtalbot over 1 year ago - 3 comments
Labels: enhancement

#58 - Ability to match parameters of BLAST as per the web app

Issue - State: open - Opened by vkullu over 1 year ago - 2 comments
Labels: enhancement

#54 - Update enrichr.md

Pull Request - State: closed - Opened by DylanLawless over 1 year ago - 1 comment

#53 - Add lxml package to requirements.txt dependencies

Issue - State: closed - Opened by lvbauer over 1 year ago - 1 comment

#52 - [gget_alphafold] - Feature Request - Add an option to submit a MSA instead of a protein sequence

Issue - State: open - Opened by kchennen over 1 year ago - 1 comment
Labels: enhancement

#51 - AttributeError: module 'psutil' has no attribute 'Process'

Issue - State: closed - Opened by najibveto over 1 year ago - 5 comments

#49 - gget alphafold: Add option to define jackhmmer save directory

Issue - State: open - Opened by lauraluebbert over 1 year ago
Labels: enhancement

#48 - Dev -> main

Pull Request - State: closed - Opened by lauraluebbert over 1 year ago

#47 - Setting up gget website

Pull Request - State: closed - Opened by lauraluebbert over 1 year ago

#46 - Jupyter Notebook Kernel Dies When Using gget alphafold

Issue - State: closed - Opened by tmileur over 1 year ago - 3 comments

#45 - Add Uniprot localisation data

Issue - State: closed - Opened by Nusob888 over 1 year ago - 3 comments
Labels: enhancement

#44 - Error detecting openmm

Issue - State: closed - Opened by LalitNM almost 2 years ago - 14 comments

#43 - AlphaFold Multimer

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

#42 - dev -> main gget pdb

Pull Request - State: closed - Opened by lauraluebbert almost 2 years ago - 1 comment

#41 - Keyerror: "0000:query"

Issue - State: closed - Opened by sharzil1994 almost 2 years ago - 5 comments

#40 - Updated alphafold output to include pLDDT

Pull Request - State: closed - Opened by lauraluebbert almost 2 years ago

#38 - pdb module

Issue - State: closed - Opened by sbliven almost 2 years ago - 2 comments
Labels: enhancement

#37 - openmm=7.5.1 is no longer available from conda-forge.

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

#36 - Fails to depict and answer the polymeric forms

Issue - State: closed - Opened by Harpreet525 almost 2 years ago - 4 comments

#35 - AlphaFold model parameters download error

Issue - State: closed - Opened by EvoEpi almost 2 years ago - 3 comments

#34 - Frozen terminal

Issue - State: closed - Opened by lt11 almost 2 years ago - 1 comment

#33 - Error running alphafold

Issue - State: closed - Opened by xinyangbing almost 2 years ago - 5 comments