X-lab-3D PANDORA issues

X-lab-3D / PANDORA

MODELLER-based, anchor restrained, Peptide-MHC Modelling pipeline

Apache License 2.0

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issues

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Update README.md for MHCII example

#259 FarzanehParizi opened 1 week ago
2
The database.pkl disappears when uploaded to zenodo because it's not in a subfolder of the database.

#258 DarioMarzella opened 6 months ago
0
Fix docs failing tag

#257 DarioMarzella opened 6 months ago
0
Add M_chain_seq and N_chain_seq arguments for command line commands

#256 DarioMarzella opened 6 months ago
0
Add PANDORA v2.0 publication reference to README

#255 DarioMarzella opened 6 months ago
0
Use MHC sequence for netmhcpan prediction instead of allele name

#254 DarioMarzella opened 6 months ago
0
User-defined MHC sequence

#253 bsb2014 closed 10 months ago
8
Add create database folders step to database generation

#252 DarioMarzella closed 10 months ago
0
Add exception and folder creation to Database.fetch_database()

#251 DarioMarzella closed 10 months ago
0
Blast version

#250 bsb2014 closed 10 months ago
30
missing file: allelenames

#249 cbaakman closed 1 year ago
1
Update development to master

#248 DarioMarzella closed 1 year ago
0
Update new_fix_lrmsd to development

#247 DarioMarzella closed 1 year ago
0
Update new_fix_lrmsd to master

#246 DarioMarzella closed 1 year ago
0
Adapt pytest so the CI run does not fail if IMGT.org is not available

#245 DarioMarzella opened 1 year ago
0
Update hotfix branch to master

#244 DarioMarzella closed 1 year ago
0
the users should not be allowed to enter both MHC allele name and MHC sequence

#243 LilySnow opened 1 year ago
0
pdb files created by PANDORA do not have a properly formatted HEADER

#242 DaniBodor opened 1 year ago
3
Fix typo in tutorial

#241 jonasfoe closed 1 year ago
0
Update master branch to v2.0.0-beta2

#240 DarioMarzella closed 1 year ago
0
Issue 235

#239 DarioMarzella closed 1 year ago
0
Merge branch from PR 237

#238 DarioMarzella closed 1 year ago
0
pandora-wrapper fixes

#237 jonasfoe closed 1 year ago
1
Add fully flexible modeling

#236 DarioMarzella closed 1 year ago
0
wrapper script

#235 GuidoLeoni closed 6 months ago
6
Redundant align_peptides functions between Align.py and Modelling_functions.py

#234 DarioMarzella opened 1 year ago
0
Update zenodo link. Hotfix cmd_pandora commands and defsault database…

#233 DarioMarzella closed 1 year ago
0
Update fully_flexible to latest development

#232 DarioMarzella closed 1 year ago
0
Add Beta-2 microglobulin

#231 DarioMarzella closed 1 year ago
0
PANDORA does not stop when no anchors are found

#230 LarsM14 opened 1 year ago
1
Neoantigens from SNV

#229 GuidoLeoni closed 1 year ago
1
Add Docker recipe and instruction.

#228 DarioMarzella closed 1 year ago
0
Make sure to go back to previous wdir whenever os.chdir is used, exce…

#227 DarioMarzella closed 1 year ago
0
Improve cmd_run_pandora allele name help string

#226 DarioMarzella closed 1 year ago
0
Docker

#225 jcgrenier closed 1 year ago
16
running code changes the working directory

#224 npqst closed 1 year ago
0
Add cmd_pandora.py. Update README.

#223 DarioMarzella closed 1 year ago
1
Fix conda and pip installation. Move database default location. Add command line option to retrieve external database.

#222 DarioMarzella closed 1 year ago
0
Folder BLAST_databases does not exist when building database

#221 heleensev closed 1 year ago
2
Remove all_IDs file at the end of the database construction

#220 DarioMarzella closed 6 months ago
0
Add warning in case users input both allele name and sequence

#219 DarioMarzella opened 1 year ago
0
FileNotFoundError's when building the database

#218 cbaakman closed 1 year ago
2
installer specification problems

#217 cbaakman closed 1 year ago
2
Rename mhcseqs files and add blast database folder.

#216 DarioMarzella closed 1 year ago
0
Fixes to claculate LRMSD to match the atoms

#215 FarzanehParizi closed 1 year ago
0
Fix redundant imports in the package

#214 gcroci2 closed 1 year ago
3
Restructure imports

#213 DarioMarzella closed 1 year ago
0
Add PMHC.__init__.py and remove obsolete IMGT retrieving module

#212 DarioMarzella closed 1 year ago
0
change archiving so that only the case folder (one level) will be included inside the .tar files

#211 heleensev closed 1 year ago
0
Add generate_database.py to the pre-release

#210 DarioMarzella closed 1 year ago
0