theislab / cellrank2_reproducibility Goto Github PK

Description

The scEU-seq data needs to be analysed using dynamo. This includes velocity information, fixed point analysis, and least action path analysis.

Description

Using plot_states to save a PDF produces an unreadable file due to dpi being specified. Instead of using dpi=400 as a default, it should be set to matplotlib's "figure".

Description

To adjust the DPI value used when saving figures, dpi needs to be added as an argument to plot_states.

Description

Add GitHub actions CI to check linting of scripts and notebooks.

Description

The README of the repository and index page of the rendered jupyter book are currently out of sync after #43.

Description

We need to add the reproducibility notebooks for the NeurIPS analysis using the PseudotimeKernel.

Description

Add TSI metric for each dataset analysed.

Description

• Rename cytotrace_vs_cr2_data_perparation.ipynb as the notebook contains both data preparation and the actual score analysis
• Remove redundant notebooks

Description

To compare macrostates (terminal states) based on different kernels, the purity w.r.t the clusters based on which they are annotated can be used. To this end, we need one function to compute the state purity, and one function to visualize it.

Description

Add notebooks to identify initial states in datasets instead of terminal states.

Descriptions

• The current dependencies do not install all required packages (wot and dynamo are missing)
• The installation instructions should be updated to install CellRank 2 via conda

Description

• Update README to include reference to CellRank 2 preprint
• Render repository as Jupyter book

Description

Set up generic project structure with pre-commit hooks, pyproject.toml file, directories for data, figures, notebooks, README, etc.

Description

ATM, the data/ and figures/ directory are note ignored by git. The corresponding lines are commented out in .gitignore.

Description

Compare the CR2 kernels to an RNA velocity-based workflow.

When installing cellrank/cellrank2 using conda-forge, even following the directions from your repository with:

conda install -c conda-forge cellrank

I get an ImportError .... : undefined symbol: H5Pget_fapl_direct: error when trying import cellrank as cr in my Jupyter notebook.

However, if I install everything in pip, there's no issues at all.

Thanks!

Description

Remove the plot_states function and rely on the estimator method plot_macrostates, instead, after it has been updated to match plot_states.

Description

Update colors used to compare methods for analysing the scEU-seq intestinal organoid data.

Description

To easily check how a given set of gene ranks among drivers towards a macrostate, a corresponding function is needed. The function can/should also be able to quantify how many of the provided genes rank below a given threshold (e.g. among the top 100 drivers).

Description

We need to add the reproducibility notebooks to

• construct the real-time-informed pseudotime and the accompanying analyses,
• analyze the pharyngeal endoderm development data.

Description

We need to add the reproducibility notebooks

• for the embryoid body analysis using the CytoTRACEKernel.
• for comparing the CytoTRACEKernel to the original CytoTRACE study

Description

The column "obs_col" is defined multiple times.

Description

To compute a real-time-informed pseudotime, the transition matrix needs to be symmetrized to apply DPT on it. A corresponding helper function get_symmetric_transition_matrix needs to be implemented.

Description

• Use estimator's plot_macrostate function directly instead of custom plot_states.
• Use pathlib to make directories instead of os.
• Add variable FIGURE_FORMAT.

Description

To plot state (macrostates, terminal states) purity with a custom order, the plot_state_purity function needs to be updated/generalized.

Description

To analyze gene trends, a pseudotime needs to be constructed for the scEU-seq data.

Description

To easily and comprehensively visualize identified macrostates or terminal states, they can be plotted with an outline on a given embedding. To do so (and reduce duplicate code), a corresponding plotting function needs to be implemented.

Description

Add or update notebooks to highlight TSI and CBC scores.

Description

We need to add the reproducibility notebooks to

• run the metabolic labeling analysis pipeline on the intestinal organoid dataset with our approach,
• run dynamo on the intestinal organoid dataset with dynamo,
• run the standard RNA velocity pipeline on the intestinal organoid dataset.

Description

The currently rendered Jupyter book of the repo does not include the notebooks of the hematopoiesis and embryoid body development analysis. The issue are incorrect paths to the respective files.

Description

Imports from cr2 are not possible because of an ill-defined __init__.py file.

from cr2 import running_in_notebook

File [/cellrank2_reproducibility/src/cr2/__init__.py:1]
----> 1 from utils import running_in_notebook
      3 __all__ = ["running_in_notebook"]

ModuleNotFoundError: No module named 'utils'