Bertinus/FLeCS

Issues

• Write tests

  #27 opened 9 months ago by Bertinus
  1

• Write scripts to download the external datasets automatically

  #21 opened 9 months ago by Bertinus
  0

• Add TF motif information from CIS-BP

  #11 opened 9 months ago by Bertinus
  3

• Write documentation

  #24 opened 9 months ago by Bertinus
  1

• test for `get_edges` and `interventions` -- watch for side effects or reallocation of memory.

  #26 opened 9 months ago by josephdviviano
  4

• Figure out how we can integrate ATAC-seq

  #37 opened 9 months ago by Bertinus
  1

• Save / Load CellPop objects

  #41 opened 9 months ago by Bertinus
  0

• Add a virus perturbation

  #36 opened 9 months ago by Bertinus
  2

• Build an antisense oligo intervention, as well as a drug intervention

  #29 opened 9 months ago by Bertinus
  0

• Have an interface with Scanpy (return adata objects)

  #45 opened 9 months ago by Bertinus
  1

• Review how other simulators have been validated

  #49 opened 9 months ago by Bertinus
  0

• Change architecture of the intervention code

  #50 opened 9 months ago by Bertinus
  0

• Start a presentation notebook

  #10 opened 2 years ago by Bertinus
  6

• __repr__ method for NodeSet / EdgeSet / CellPop should show all attributes

  #42 opened 2 years ago by Bertinus
  0

• Figure out if we can encode communication between cells

  #38 opened 2 years ago by Bertinus
  1

• Have an Active Learning benchmark

  #39 opened 2 years ago by Bertinus
  1

• Add Typing and torchTyping information

  #31 opened 2 years ago by Bertinus
  1

• Add protein binding information from the String database

  #9 opened 2 years ago by Bertinus
  6

• Add an option to choose the initial distribution of cell states

  #33 opened 2 years ago by Bertinus
  1

• Add SDE trajectories

  #32 opened 2 years ago by Bertinus
  1

• Build out mutation abstract class

  #8 opened 2 years ago by Bertinus
  2

• Write CellPop class with splicing information

  #18 opened 2 years ago by Bertinus
  1

• Make CellPop inherit from torch.nn.Module

  #28 opened 2 years ago by Bertinus
  1

• Write and test a simple pipeline in which the parameters of a CellPopulation object are learnt

  #19 opened 2 years ago by Bertinus
  1

• `NodeSet` and `EdgeSet` should have a `setattr` method

  #12 opened 2 years ago by josephdviviano
  2

• Add commands to create documentation using mkdocs in the README

  #23 opened 2 years ago by Bertinus
  1

• Review Pull Request

  #20 opened 2 years ago by Bertinus
  2

• Ways to load/save cell population objects

  #6 opened 2 years ago by josephdviviano
  1

• Write down generic methods s.a. MessagePassing, ExponentialDecay etc.

  #14 opened 2 years ago by Bertinus
  2

• Build out intervention abstract class

  #2 opened 2 years ago by josephdviviano
  1

• Review EdgeSet, NodeSet, CellPopulation files

  #4 opened 2 years ago by josephdviviano
  1

• Review `data/interaction_data.py`

  #5 opened 2 years ago by josephdviviano
  2

• Add examples for all objects.

  #7 opened 2 years ago by josephdviviano
  1

• Build minimal demo notebook

  #3 opened 2 years ago by josephdviviano
  0