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Bertinus
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FLeCS
Flexible and Learnable Cell Simulator
MIT License
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Added interventional model
#53
Bertinus
closed
11 months ago
0
Added validation code and notebooks
#52
Bertinus
closed
11 months ago
0
Intervention added to base class
#51
josephdviviano
closed
11 months ago
1
Change architecture of the intervention code
#50
Bertinus
closed
11 months ago
0
Review how other simulators have been validated
#49
Bertinus
closed
11 months ago
0
Mutations
#48
josephdviviano
closed
1 year ago
0
Template
#47
josephdviviano
closed
1 year ago
0
Bertinus/notebooks
#46
Bertinus
closed
1 year ago
0
Have an interface with Scanpy (return adata objects)
#45
Bertinus
closed
11 months ago
1
to sync
#44
josephdviviano
closed
1 year ago
0
jdv/test refactor
#43
josephdviviano
closed
1 year ago
0
__repr__ method for NodeSet / EdgeSet / CellPop should show all attributes
#42
Bertinus
closed
1 year ago
0
Save / Load CellPop objects
#41
Bertinus
closed
11 months ago
0
Documentation update
#40
Bertinus
closed
1 year ago
0
Have an Active Learning benchmark
#39
Bertinus
closed
1 year ago
1
Figure out if we can encode communication between cells
#38
Bertinus
closed
1 year ago
1
Figure out how we can integrate ATAC-seq
#37
Bertinus
closed
11 months ago
1
Add a virus perturbation
#36
Bertinus
closed
11 months ago
2
Simplification of Set classes
#35
Bertinus
closed
1 year ago
0
Added basic string database
#34
josephdviviano
closed
1 year ago
1
Add an option to choose the initial distribution of cell states
#33
Bertinus
closed
1 year ago
1
Add SDE trajectories
#32
Bertinus
closed
1 year ago
1
Add Typing and torchTyping information
#31
Bertinus
closed
1 year ago
1
Simplified the procedure to get a trainable CellPop object
#30
Bertinus
closed
1 year ago
0
Build an antisense oligo intervention, as well as a drug intervention
#29
Bertinus
closed
11 months ago
0
Make CellPop inherit from torch.nn.Module
#28
Bertinus
closed
1 year ago
1
Write tests
#27
Bertinus
closed
11 months ago
1
test for `get_edges` and `interventions` -- watch for side effects or reallocation of memory.
#26
josephdviviano
closed
11 months ago
4
Jdv/selfdocumenting
#25
josephdviviano
closed
1 year ago
0
Write documentation
#24
Bertinus
closed
11 months ago
1
Add commands to create documentation using mkdocs in the README
#23
Bertinus
closed
1 year ago
1
Jdv/selfdocumenting
#22
josephdviviano
closed
1 year ago
0
Write scripts to download the external datasets automatically
#21
Bertinus
closed
11 months ago
0
Review Pull Request
#20
Bertinus
closed
1 year ago
2
Write and test a simple pipeline in which the parameters of a CellPopulation object are learnt
#19
Bertinus
closed
1 year ago
1
Write CellPop class with splicing information
#18
Bertinus
closed
1 year ago
1
Modified the demo for defining a custom CellPopulation object
#17
Bertinus
closed
1 year ago
2
Environment installation
#16
Bertinus
closed
1 year ago
0
Jdv/demo
#15
josephdviviano
closed
1 year ago
0
Write down generic methods s.a. MessagePassing, ExponentialDecay etc.
#14
Bertinus
closed
1 year ago
2
Jdv/cleanup
#13
josephdviviano
closed
1 year ago
1
`NodeSet` and `EdgeSet` should have a `setattr` method
#12
josephdviviano
closed
1 year ago
2
Add TF motif information from CIS-BP
#11
Bertinus
closed
11 months ago
3
Start a presentation notebook
#10
Bertinus
opened
1 year ago
6
Add protein binding information from the String database
#9
Bertinus
closed
1 year ago
6
Build out mutation abstract class
#8
Bertinus
closed
1 year ago
2
Add examples for all objects.
#7
josephdviviano
closed
1 year ago
1
Ways to load/save cell population objects
#6
josephdviviano
closed
1 year ago
1
Review `data/interaction_data.py`
#5
josephdviviano
closed
1 year ago
2
Review EdgeSet, NodeSet, CellPopulation files
#4
josephdviviano
closed
1 year ago
1
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