CellRank's reproducibility repository.

Last update: Oct 08, 2022

Overview

CellRank's reproducibility repository

We believe that reproducibility is key and have made it as simple as possible to reproduce our results. Please either open an issue or contact as at [email protected] should you experience difficulties reproducing any result.

Manuscript, code and data

CellRank is published in Nature Methods and the software package can be found at our main website, cellrank.org. Raw published data is available from the Gene Expression Omnibus (GEO) under accession codes:

Processed data, including spliced and unspliced count abundances, is available on figshare. To ease reproducibility, our data examples can also be accessed through CellRank's dataset interface.

Navigating this repository

We've organized this repository along the categories below. For each item, you can click the link under nbviewer to open the notebook in the browser using nbviewer. There is no 1-1 mapping from figures to notebooks - some notebooks produce panels for several figures, and some figures contain panels from several notebooks. The tables we provide here make the connection between figures and notebooks explicit. At the top of each notebook, we indicate the package versions we use.

Results

Main Figures

Figure	nbviewer	Notebook Path
Fig. 1	link	path
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Fig. 5 Palantir	link	path
Fig. 5 STEMNET	link	path
Fig. 5 Velocyto	link	path
Fig. 5 FateID	link	path
Fig. 6	link	path

Extended Data Figures

Figure	nbviewer	Notebook Path
Extended Data Fig. 1	NA (toy data)	NA (toy data)
Extended Data Fig. 2	link	path
Extended Data Fig. 3	link	path
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Extended Data Fig. 9	link	path
Extended Data Fig. 10	link	path

Supplementary Figures

Figure	nbviewer	Notebook Path
Supplementary Fig. 1	link	path
Supplementary Fig. 2	link	path
Supplementary Fig. 3	link	path
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Supplementary Fig. 12	link1 link2	path1 path2
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Supplementary Fig. 17	NA (microscopy results)	NA (microscopy results)

Supplementary Tables

Table	nbviewer	Notebook Path
Supplementary Tab. 1	link	path
Supplementary Tab. 2	link	path
Supplementary Tab. 3	link	path

CellRank's reproducibility repository.

Related tags

Overview

CellRank's reproducibility repository

Manuscript, code and data

Navigating this repository

Results

Owner

Theis Lab

This is an official implementation for "PlaneRecNet".

(IEEE TIP 2021) Regularized Densely-connected Pyramid Network for Salient Instance Segmentation

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Code for the AAAI 2022 paper "Zero-Shot Cross-Lingual Machine Reading Comprehension via Inter-Sentence Dependency Graph".

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ContourletNet: A Generalized Rain Removal Architecture Using Multi-Direction Hierarchical Representation

Adversarial Autoencoders

Local Similarity Pattern and Cost Self-Reassembling for Deep Stereo Matching Networks

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A learning-based data collection tool for human segmentation

Reference implementation for Structured Prediction with Deep Value Networks

Controlling a game using mediapipe hand tracking

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StarGAN - Official PyTorch Implementation (CVPR 2018)

Easy way to add GoogleMaps to Flask applications. maintainer: @getcake

A static analysis library for computing graph representations of Python programs suitable for use with graph neural networks.

ShapeGlot: Learning Language for Shape Differentiation

A clean and scalable template to kickstart your deep learning project 🚀 ⚡ 🔥

Explanatory Learning: Beyond Empiricism in Neural Networks