gyorilab/protmapper issues and pull requests

#47 - Updates and new features

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

#46 - Bump version to update resources

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

#45 - Update UniProt client due to new UniProt API

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

#44 - Migrate UniProt resources to new web service

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

#43 - Use legacy UniProt web service

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

#42 - Refactor loading FASTA into two functions

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

#41 - Replace RDF with XML in UniProt client

Pull Request - State: closed - Opened by bgyori about 3 years ago - 1 comment

#40 - Rdflib issue on Github actions

Issue - State: closed - Opened by bgyori about 3 years ago - 1 comment

#39 - Add lookup by MGI and RGD name

Pull Request - State: closed - Opened by cthoyt about 3 years ago

#38 - Improve protein name extraction and compress resource files

Pull Request - State: closed - Opened by bgyori about 3 years ago

#37 - Add citation bibtex to readme

Pull Request - State: closed - Opened by cthoyt about 3 years ago

#36 - Add Entrez mappings for non-human entries

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

#35 - Use PyStow to locate resource directory

Pull Request - State: closed - Opened by cthoyt over 3 years ago - 7 comments

#34 - Return protein name if gene name is not available

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

#33 - Better gene names and fragment features from UniProt

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

#32 - Include taxonomy ID for each protein

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

#31 - Update resources

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

#30 - Problematic Entrez ID

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

#29 - Add support for Entrez mappings

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

#28 - Add entrez identifier conversions

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

#27 - Add get feature of function

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

#26 - Integrate protein post-processing features and Sars-CoV-2 entries

Pull Request - State: closed - Opened by bgyori over 4 years ago - 1 comment

#25 - Sarscov2 UP pre-release

Pull Request - State: closed - Opened by kkaris over 4 years ago - 1 comment

#24 - Add broader error handling for sequence lookups

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

#23 - Add smoke tests for CLI

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

#22 - Handle isoform suffix in UniProt client

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

#21 - Add a CLI for the protmapper

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

#20 - Add mapping from UP ID directly to HGNC ID

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

#19 - Fix handling multiple returned UP IDs for an HGNC ID

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

#18 - Issue when mapping peptides to uniprot non-base isoforms

Issue - State: closed - Opened by FFroehlich over 5 years ago - 6 comments

#17 - fix map_peptide_to_human_ref typehint

Pull Request - State: closed - Opened by FFroehlich over 5 years ago - 1 comment

#16 - Issues when mapping non-unique HGNC ids

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

#15 - Dockerize the protmapper

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

#14 - Improve argument and error handling in REST API

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

#13 - Use version in resource downloads

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

#12 - Implement mapping based on signal peptides

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

#11 - Peptide-based site remapping and isoform-specific IDs

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

#10 - Fix sequence resource downloads

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

#9 - Error in refseq download

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

#8 - Add documentation

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

#7 - Make resource downloads with nosetests work on Python 3.5

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

#6 - Resource management, UniProt client

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

#5 - Handle errors, including sequence retrieval and invalid gene names

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

#4 - Use jsonify to send responses in REST api

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

#3 - Setup downloads resource files

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

#2 - Add docstrings for MappedSite

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

#1 - Simple REST API

Pull Request - State: closed - Opened by bgyori almost 6 years ago - 3 comments

GitHub / gyorilab/protmapper issues and pull requests