KohlbacherLab/epytope issues and pull requests

#100 - Update pypi-publish.yml

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

#99 - Update pypi-publish.yml

Pull Request - State: closed - Opened by jonasscheid 9 months ago - 4 comments

#98 - Release 3.4.0

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

#97 - Prepare release 3.4.0

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

#96 - Add netmhciipan 4.3 interface

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

#95 - Add netmhciipan 4.3 interface

Issue - State: open - Opened by jonasscheid 10 months ago
Labels: enhancement

#94 - update git hub actions versions

Pull Request - State: closed - Opened by christopher-mohr 10 months ago - 1 comment

#93 - Fix netmhc len restriction, add netmhciipan 4.2 interface

Pull Request - State: closed - Opened by jonasscheid 10 months ago - 3 comments

#92 - Add netmhciipan 4.2 interface

Issue - State: open - Opened by jonasscheid 10 months ago
Labels: enhancement

#91 - NetMHCpan: False peptide min/max boundaries

Issue - State: open - Opened by jonasscheid about 1 year ago - 5 comments
Labels: bug

#90 - Update pypi-publish.yml

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

#89 - Update version to 3.3.1 in setup.py

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

#88 - Release 3.3.1

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

#87 - Prepare release

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 6 comments

#86 - merge Develop into feature branch

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

#85 - Pin working pandas versions

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

#84 - Failure to parse netMHCpan 4.0 output

Issue - State: closed - Opened by e-dorigatti over 1 year ago - 7 comments
Labels: enhancement

#83 - Fix mouse-specific PSSMs

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

#82 - Predicting on mouse alleles fails due to erroneous nomenclature conversion

Issue - State: closed - Opened by jonasscheid almost 2 years ago
Labels: bug

#81 - Update setup.py

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

#80 - Release 3.3.0

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

#79 - Change to PyVCF3

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

#78 - Fix errorneous supported alleles

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

#77 - Release 3.2.0

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

#76 - Release 3.2.0

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

#75 - Improve function to check peptide origin

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

#74 - Add function for peptides to check if created by variant

Pull Request - State: closed - Opened by christopher-mohr about 2 years ago

#73 - Fix netmhcii4.0 parser

Pull Request - State: closed - Opened by jonasscheid about 2 years ago

#72 - NetMHCIIpan 4.0 parser returns same scores for different alleles

Issue - State: closed - Opened by jonasscheid about 2 years ago
Labels: bug

#71 - Update uniprot adapter

Pull Request - State: closed - Opened by christopher-mohr about 2 years ago

#70 - remove HLAtyping and distance2self tests, update CHANGELOG

Pull Request - State: closed - Opened by christopher-mohr about 2 years ago

#69 - Update MartsAdapter

Pull Request - State: closed - Opened by christopher-mohr about 2 years ago - 2 comments

#68 - Release 3.1.0

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

#67 - Release 3.1.0

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

#66 - Add netMHCIIpan 4.1 interface

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

#65 - Include NetMHCIIpan 4.1 interface

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

#64 - Fix protobuf version for tests, prepare docs for 3.1.0 release

Pull Request - State: closed - Opened by jonasscheid over 2 years ago - 3 comments

#63 - Outsource supported alleles

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

#62 - Update supportedAlleles of syfpeithi

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

#61 - Outsource supportedAlleles of predictors

Issue - State: closed - Opened by jonasscheid over 2 years ago - 1 comment
Labels: enhancement

#60 - Missing alleles in supportedAlleles set of syfpeithi

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

#59 - Add interface for netMHCpan 4.1

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

#58 - Add check for BioMart transcript sequence availability

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

#57 - Improve MartsAdapter and support different BioMart references

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

#56 - Add interface for NetMHCpan 4.1

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

#55 - Protein generation from transcript fails when (coding) transcript sequence is unavailable

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

#54 - Add interface for MHCflurry 2.0.x

Pull Request - State: open - Opened by christopher-mohr over 2 years ago
Labels: donotmerge

#53 - Fix ANN predictor results

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

#52 - ANN predictor output returns peptide strings instead of peptide objects

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

#51 - epytope installation fails for python >3.7

Issue - State: open - Opened by christopher-mohr over 2 years ago - 1 comment
Labels: bug

#50 - Improve/update documentation

Pull Request - State: closed - Opened by christopher-mohr almost 3 years ago - 1 comment
Labels: documentation

#49 - Release 3.0.0

Pull Request - State: closed - Opened by christopher-mohr almost 3 years ago

#48 - Wrong mouse allele string in supported alleles of external tools

Issue - State: closed - Opened by jonasscheid almost 3 years ago
Labels: bug

#47 - Add interface for mhcflurry v2.0.0

Issue - State: open - Opened by christopher-mohr almost 3 years ago
Labels: enhancement

#46 - Fixed issues #38, #44 and #45

Pull Request - State: closed - Opened by jonasscheid almost 3 years ago

#45 - Current Class2 external tools don't predict CombinedAlleles

Issue - State: closed - Opened by jonasscheid almost 3 years ago - 2 comments
Labels: bug

#44 - Include interface of NetMHCII 2.3 and NetMHCIIpan 4.0

Issue - State: closed - Opened by jonasscheid almost 3 years ago
Labels: enhancement

#43 - Introduce new Class for ScoreType to replace hardcoded "Score" and "Rank" metrics

Issue - State: open - Opened by jonasscheid almost 3 years ago
Labels: enhancement

#42 - Add rank metric #15

Pull Request - State: closed - Opened by jonasscheid almost 3 years ago - 4 comments

#41 - Rank support of multiple prediction tools #15

Pull Request - State: closed - Opened by jonasscheid about 3 years ago - 4 comments

#40 - Upload syfpeithi latest matrices

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

#39 - Upload latest syfpeithi matrices

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

#38 - EpitopePrediction ANN Classes create new Allele objects on predict

Issue - State: closed - Opened by b-schubert about 3 years ago - 4 comments
Labels: bug

#37 - NetMHCIIpan 3.1 class is missing crucial methods

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

#36 - Remove support of old netmhc version dependent on Python 2.x

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

#35 - Change PyPI CD trigger to published release

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

#34 - Add a changelog

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

#33 - Reduce version to 3.0.0rc1

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

#32 - Develop

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

#31 - Add pypi GH action

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

#30 - Fix master / main branch naming in GH action

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

#29 - Version bump 3.0.0rc2

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

#28 - Readme/typos

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

#27 - Release 3.0.0rc1

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

#26 - License

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

#25 - Refactor CI: Install all dependencies via pip

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

#24 - Add keras dependency

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

#23 - Rename FRED-2 to epytope

Pull Request - State: closed - Opened by lkuchenb over 3 years ago - 1 comment

#22 - Improve netmhc* error handling

Issue - State: open - Opened by lkuchenb over 3 years ago
Labels: enhancement

#21 - Rename Package

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

#20 - Logging

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

#19 - Logging

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

#18 - Fix external (net*) epitope prediction error and tempfile handling

Pull Request - State: closed - Opened by lkuchenb over 3 years ago
Labels: bug

#17 - Fix Invalid subprocess handling and mhcflurry polluting stdout

Pull Request - State: closed - Opened by lkuchenb over 3 years ago
Labels: bug

#16 - Fix epitope prediction 2to3 bugs and tests

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

#15 - Support multiple epitope prediction scores per tool

Issue - State: closed - Opened by lkuchenb over 3 years ago - 14 comments
Labels: enhancement

#14 - Extend tests to additional Python versions

Issue - State: closed - Opened by lkuchenb over 3 years ago - 1 comment
Labels: wontfix

#13 - [2to3] Fix writing of ANN output to file

Pull Request - State: closed - Opened by lkuchenb over 3 years ago - 1 comment

#12 - Notebooks + doc require porting to Python 3

Issue - State: closed - Opened by lkuchenb over 3 years ago - 4 comments
Labels: documentation, enhancement

#11 - Fix hard coded python version in CI, remove broken versions

Pull Request - State: closed - Opened by lkuchenb almost 4 years ago - 1 comment

#10 - Naming

Issue - State: closed - Opened by b-schubert almost 4 years ago - 6 comments

#9 - 2to3conv

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

#8 - Should HLA typing remain a part of FRED?

Issue - State: closed - Opened by lkuchenb almost 4 years ago - 3 comments
Labels: question

#7 - HLA Typing tests have hard coded local paths

Issue - State: closed - Opened by lkuchenb almost 4 years ago
Labels: bug, test

#6 - Add CI for external tools

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

#5 - Add external ci

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

#4 - 2to3conv

Pull Request - State: closed - Opened by antschum almost 4 years ago - 1 comment

#3 - 2to3conv

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

#2 - Enforce biopythion version that supports python 2.7

Pull Request - State: closed - Opened by lkuchenb almost 4 years ago - 1 comment

#1 - Fix CI, move to GH actions

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

GitHub / KohlbacherLab/epytope issues and pull requests