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
Extended Data Fig. 4	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

An official repository for Paper "Uformer: A General U-Shaped Transformer for Image Restoration".

[NeurIPS 2021] Shape from Blur: Recovering Textured 3D Shape and Motion of Fast Moving Objects

Rlmm blender toolkit - A set of tools to streamline level generation in UDK straight from Blender

Danfeng Hong, Lianru Gao, Jing Yao, Bing Zhang, Antonio Plaza, Jocelyn Chanussot. Graph Convolutional Networks for Hyperspectral Image Classification, IEEE TGRS, 2021.

An introduction to bioimage analysis - http://bioimagebook.github.io

Multi-modal co-attention for drug-target interaction annotation and Its Application to SARS-CoV-2

Hierarchical Motion Encoder-Decoder Network for Trajectory Forecasting (HMNet)

Multi Agent Reinforcement Learning for ROS in 2D Simulation Environments

Real-Time Multi-Contact Model Predictive Control via ADMM

BERT model training impelmentation using 1024 A100 GPUs for MLPerf Training v1.1

Readings for "A Unified View of Relational Deep Learning for Polypharmacy Side Effect, Combination Therapy, and Drug-Drug Interaction Prediction."

Data loaders and abstractions for text and NLP

Classification of ecg datas for disease detection

Lung Pattern Classification for Interstitial Lung Diseases Using a Deep Convolutional Neural Network

Multi-Objective Loss Balancing for Physics-Informed Deep Learning

Boundary-aware Transformers for Skin Lesion Segmentation

FairFuzz: AFL extension targeting rare branches

ViDT: An Efficient and Effective Fully Transformer-based Object Detector

Official repository for Fourier model that can generate periodic signals

Activity tragle - Google is tracking everything, we just look at it