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. 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

We envision models that are pre-trained on a vast range of domain-relevant tasks to become key for molecule property prediction

A Python type explainer!

Implementation of Transformer in Transformer, pixel level attention paired with patch level attention for image classification, in Pytorch

Parametric Contrastive Learning (ICCV2021)

DeepFill v1/v2 with Contextual Attention and Gated Convolution, CVPR 2018, and ICCV 2019 Oral

Memory-efficient optimum einsum using opt_einsum planning and PyTorch kernels.

Adaout is a practical and flexible regularization method with high generalization and interpretability

[CVPR 2022 Oral] MixFormer: End-to-End Tracking with Iterative Mixed Attention

ImageBART: Bidirectional Context with Multinomial Diffusion for Autoregressive Image Synthesis

Official PyTorch implementation of "Contrastive Learning from Extremely Augmented Skeleton Sequences for Self-supervised Action Recognition" in AAAI2022.

Rethinking of Pedestrian Attribute Recognition: A Reliable Evaluation under Zero-Shot Pedestrian Identity Setting

NER for Indian languages

Simple and Distributed Machine Learning

Automatic Image Background Subtraction

The InterScript dataset contains interactive user feedback on scripts generated by a T5-XXL model.

A lossless neural compression framework built on top of JAX.

This application explain how we can easily integrate Deepface framework with Python Django application

A PyTorch implementation for PyramidNets (Deep Pyramidal Residual Networks)

6D Grasping Policy for Point Clouds

A small demonstration of using WebDataset with ImageNet and PyTorch Lightning