Ecosyste.ms: Issues

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

GitHub / X-lab-3D/PANDORA issues and pull requests

#292 - How to create model using a user input template.pdb file

Issue - State: open - Opened by Mayjig 4 months ago - 1 comment
Labels: question

#291 - Update README.md

Pull Request - State: closed - Opened by DTRademaker 4 months ago

#290 - Update meta.yaml

Pull Request - State: closed - Opened by DTRademaker 4 months ago

#289 - Development

Pull Request - State: closed - Opened by DTRademaker 4 months ago

#288 - Development

Pull Request - State: closed - Opened by DTRademaker 4 months ago

#287 - Rev2dev

Pull Request - State: closed - Opened by DTRademaker 4 months ago

#286 - Rev2dev

Pull Request - State: closed - Opened by DTRademaker 4 months ago

#285 - Development

Pull Request - State: closed - Opened by DTRademaker 4 months ago

#284 - Reverse2development

Pull Request - State: closed - Opened by DTRademaker 4 months ago

#283 - Update reverse2development to latest development

Pull Request - State: closed - Opened by DarioMarzella 4 months ago - 1 comment

#282 - Reverse2development

Pull Request - State: closed - Opened by DTRademaker 4 months ago

#281 - Reverse2development

Pull Request - State: closed - Opened by DTRademaker 4 months ago

#280 - setting the anchor points to '0,8' does not lead to an exception

Issue - State: open - Opened by cbaakman 4 months ago - 1 comment
Labels: Warning/Exception needed

#279 - Update README.md

Pull Request - State: closed - Opened by DarioMarzella 4 months ago

#278 - Reverse peptide mhcii

Pull Request - State: closed - Opened by DTRademaker 4 months ago

#276 - Add test for database automatic fetching from zenodo

Issue - State: open - Opened by DarioMarzella 4 months ago
Labels: Code quality

#273 - Conda installation failing due to ERROR 404 missing current_repodata.json

Issue - State: open - Opened by DarioMarzella 5 months ago
Labels: wontfix, Installation

#272 - update version number in meta.yaml

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

#271 - Github automatic testing fail

Issue - State: closed - Opened by DarioMarzella 5 months ago - 1 comment
Labels: bug

#270 - Update to version 2.0.0

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

#269 - Fix GitHub pytest

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

#267 - Hotfix docs building

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

#266 - Edit dbfolders structure zotero

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

#265 - Merge development into master

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

#264 - Update development to latest master changes

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

#263 - Revert "Reverse peptide mhcii"

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

#262 - Create Generate_reverse_templates.py

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

#261 - Reverse peptide mhcii

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

#260 - conda installation fails

Issue - State: closed - Opened by LilySnow 5 months ago - 7 comments
Labels: bug

#259 - Update README.md for MHCII example

Pull Request - State: closed - Opened by FarzanehParizi 6 months ago - 2 comments

#257 - Fix docs failing tag

Issue - State: closed - Opened by DarioMarzella 12 months ago - 1 comment

#256 - Add M_chain_seq and N_chain_seq arguments for command line commands

Issue - State: open - Opened by DarioMarzella 12 months ago
Labels: enhancement

#255 - Add PANDORA v2.0 publication reference to README

Issue - State: open - Opened by DarioMarzella 12 months ago
Labels: documentation

#254 - Use MHC sequence for netmhcpan prediction instead of allele name

Issue - State: open - Opened by DarioMarzella 12 months ago
Labels: enhancement

#253 - User-defined MHC sequence

Issue - State: closed - Opened by bsb2014 over 1 year ago - 8 comments

#252 - Add create database folders step to database generation

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

#251 - Add exception and folder creation to Database.fetch_database()

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

#250 - Blast version

Issue - State: closed - Opened by bsb2014 over 1 year ago - 30 comments

#249 - missing file: allelenames

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

#248 - Update development to master

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

#247 - Update new_fix_lrmsd to development

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

#246 - Update new_fix_lrmsd to master

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

#244 - Update hotfix branch to master

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

#242 - pdb files created by PANDORA do not have a properly formatted HEADER

Issue - State: open - Opened by DaniBodor almost 2 years ago - 3 comments
Labels: enhancement

#241 - Fix typo in tutorial

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

#240 - Update master branch to v2.0.0-beta2

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

#239 - Issue 235

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

#238 - Merge branch from PR 237

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

#237 - pandora-wrapper fixes

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

#236 - Add fully flexible modeling

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

#235 - wrapper script

Issue - State: closed - Opened by GuidoLeoni almost 2 years ago - 6 comments

#234 - Redundant align_peptides functions between Align.py and Modelling_functions.py

Issue - State: open - Opened by DarioMarzella almost 2 years ago
Labels: Code quality

#232 - Update fully_flexible to latest development

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

#231 - Add Beta-2 microglobulin

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

#230 - PANDORA does not stop when no anchors are found

Issue - State: open - Opened by LarsM14 about 2 years ago - 1 comment
Labels: Warning/Exception needed

#229 - Neoantigens from SNV

Issue - State: closed - Opened by GuidoLeoni about 2 years ago - 1 comment
Labels: question

#228 - Add Docker recipe and instruction.

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

#226 - Improve cmd_run_pandora allele name help string

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

#225 - Docker

Issue - State: closed - Opened by jcgrenier about 2 years ago - 16 comments
Labels: enhancement, help wanted, Installation

#224 - running code changes the working directory

Issue - State: closed - Opened by npqst about 2 years ago

#223 - Add cmd_pandora.py. Update README.

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

#221 - Folder BLAST_databases does not exist when building database

Issue - State: closed - Opened by heleensev over 2 years ago - 2 comments

#220 - Remove all_IDs file at the end of the database construction

Issue - State: closed - Opened by DarioMarzella over 2 years ago
Labels: wontfix, book_chapter

#219 - Add warning in case users input both allele name and sequence

Issue - State: open - Opened by DarioMarzella over 2 years ago
Labels: Code quality

#218 - FileNotFoundError's when building the database

Issue - State: closed - Opened by cbaakman over 2 years ago - 2 comments

#217 - installer specification problems

Issue - State: closed - Opened by cbaakman over 2 years ago - 2 comments

#216 - Rename mhcseqs files and add blast database folder.

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

#215 - Fixes to claculate LRMSD to match the atoms

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

#214 - Fix redundant imports in the package

Pull Request - State: closed - Opened by gcroci2 over 2 years ago - 3 comments

#213 - Restructure imports

Issue - State: closed - Opened by DarioMarzella over 2 years ago
Labels: Code quality, book_chapter

#212 - Add PMHC.__init__.py and remove obsolete IMGT retrieving module

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

#210 - Add generate_database.py to the pre-release

Issue - State: closed - Opened by DarioMarzella over 2 years ago
Labels: book_chapter

#209 - Issue#204

Pull Request - State: closed - Opened by Smaassen2 over 2 years ago - 1 comment

#208 - Fix Issue 151. Update dependencies and README. Update setup.py

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

#207 - Allele name too long cause netMHCpan anchor prediction to crash

Issue - State: open - Opened by DarioMarzella over 2 years ago
Labels: bug

#206 - Fix issue 202

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

#204 - Generate defuault output directory in the current working directory

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

#203 - Missing alleles in PANDORA database can be retrieved from IMGT database

Issue - State: closed - Opened by heleensev over 2 years ago - 1 comment

#200 - Fix/update of the test_pandora.py file

Pull Request - State: closed - Opened by Smaassen2 over 2 years ago

#199 - Archiving

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

#198 - Archiving

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

#197 - Development

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

#196 - Issue 112

Pull Request - State: closed - Opened by Smaassen2 over 2 years ago - 8 comments

#195 - Development

Pull Request - State: closed - Opened by Smaassen2 over 2 years ago

#194 - Development

Pull Request - State: closed - Opened by Smaassen2 over 2 years ago

#193 - Fix Muscle version issue. Add blast to dependencies. Update README

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