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gyorilab
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pybiopax
PyBioPAX: A python implementation of the BioPAX object model
BSD 2-Clause "Simplified" License
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Update pc2 URL to use https
#53
tonywu1999
closed
6 months ago
2
model_from_pc_query Connection Aborted Error
#52
tonywu1999
closed
6 months ago
0
Enable passing encoding
#51
cthoyt
closed
1 year ago
0
UnicodeDecodeError in windows
#50
Crispae
closed
1 year ago
3
Added pathway_order and next_step to a list
#49
tmushayahama
closed
1 year ago
4
Add attributes to NucleicAcid reference BioPAX classes
#48
bgyori
closed
1 year ago
0
regionType for SequenceLocation but not NucleicAcidRegionReference
#47
quirinmanz
closed
1 year ago
2
Add global tqdm config
#46
bgyori
closed
1 year ago
1
Add py.typed
#45
bgyori
closed
1 year ago
0
Pass tqdm kwargs
#44
eggplants
closed
1 year ago
7
Provide type information
#43
eggplants
closed
1 year ago
0
Make new pypi release
#42
matthiaskoenig
closed
2 years ago
1
Notebook demonstrating model construction
#41
bgyori
closed
2 years ago
0
Adding second protein to BioPax model gives TypeError
#40
aditya-ml
closed
2 years ago
2
Improve BioPAX class attribute documentation
#39
bgyori
closed
2 years ago
0
Enable passing a list of BioPaxObject to BioPaxModel
#38
cthoyt
closed
2 years ago
0
Use empty list by default if list-type is None
#37
bgyori
closed
2 years ago
0
Example/documentation for creating BioPax from scratch
#36
matthiaskoenig
closed
2 years ago
5
Add functions to get database references from a model
#35
bgyori
closed
2 years ago
0
Add utilities for analyzing ontology terms and identifiers in a biopax file
#34
cmungall
closed
2 years ago
6
Converting BioPAX to signed directed pairwise graph
#33
agitter
closed
2 years ago
2
Fix references
#32
bgyori
closed
2 years ago
0
Add dedicated state of the field section
#31
bgyori
closed
2 years ago
0
State of the field section in JOSS paper
#30
leonweber
closed
2 years ago
1
Paper links to specific notebook version
#29
bgyori
closed
2 years ago
0
Visualizing BioPaxModels in Python?
#28
dhimmel
closed
2 years ago
1
Add source files for JOSS submission
#27
bgyori
closed
2 years ago
0
Improve testing, documentation and notebooks
#26
bgyori
closed
2 years ago
0
Synchronize contributions and setup with testing
#25
bgyori
closed
2 years ago
0
Improvements to API and docs
#24
bgyori
closed
2 years ago
0
Add Pathway Commons traversal demo notebook
#23
cthoyt
closed
2 years ago
0
API Cleanup
#22
cthoyt
closed
2 years ago
0
Add CREEDS analysis
#21
cthoyt
closed
2 years ago
1
Add ability to pass tqdm kwargs in API functions
#20
cthoyt
closed
2 years ago
2
Update types in I/O functions
#19
cthoyt
closed
3 years ago
0
Implement path search based on path string specification
#18
bgyori
closed
3 years ago
0
Fix tqdm
#17
bgyori
closed
3 years ago
0
Implement reverse links as properties
#16
bgyori
closed
3 years ago
0
Implement mixin properties and aggregate names
#15
bgyori
closed
3 years ago
0
Add additional BioPAX remote resources
#14
cthoyt
closed
3 years ago
4
Add tutorial notebook and contrib guidelines
#13
bgyori
closed
3 years ago
0
Clean up project metadata
#12
cthoyt
closed
3 years ago
0
Type annotate code
#11
cthoyt
closed
2 years ago
0
Make participants of Interactions list-like
#10
bgyori
closed
3 years ago
0
Interactions with multiple participants
#9
annaritz
closed
3 years ago
5
Migrate from Travis to GitHub Actions
#8
bgyori
closed
3 years ago
0
Allow specification of file encoding
#7
cthoyt
closed
3 years ago
1
Handle the XML-base namespace of models
#6
bgyori
closed
4 years ago
0
Handle XMLs where objects are embedded
#5
bgyori
closed
4 years ago
0
Add repr/str for a few classes
#4
bgyori
closed
4 years ago
0
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