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
Fig. 2	link	path
Fig. 3	link	path
Fig. 4	link	path
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
Extended Data Fig. 5	link	path
Extended Data Fig. 6	link	path
Extended Data Fig. 7	link	path
Extended Data Fig. 8	link	path
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
Supplementary Fig. 4	link	path
Supplementary Fig. 5	link	path
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Supplementary Fig. 12	link1 link2	path1 path2
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Supplementary Fig. 14	link	path
Supplementary Fig. 15	link	path
Supplementary Fig. 16	link	path
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

Autonomous Movement from Simultaneous Localization and Mapping

LIVECell - A large-scale dataset for label-free live cell segmentation

Tooling for GANs in TensorFlow

The first dataset of composite images with rationality score indicating whether the object placement in a composite image is reasonable.

Real-time face detection and emotion/gender classification using fer2013/imdb datasets with a keras CNN model and openCV.

Code and model benchmarks for "SEVIR : A Storm Event Imagery Dataset for Deep Learning Applications in Radar and Satellite Meteorology"

The final project of "Applying AI to 2D Medical Imaging Data" of "AI for Healthcare" nanodegree - Udacity.

An Image compression simulator that uses Source Extractor and Monte Carlo methods to examine the post compressive effects different compression algorithms have.

Misc YOLOL scripts for use in the Starbase space sandbox videogame

Huawei Hackathon 2021 - Sweden (Stockholm)

基于pytorch构建cyclegan示例

HEAM: High-Efficiency Approximate Multiplier Optimization for Deep Neural Networks

A cross-document event and entity coreference resolution system, trained and evaluated on the ECB+ corpus.

PyTorch code for EMNLP 2021 paper: Don't be Contradicted with Anything! CI-ToD: Towards Benchmarking Consistency for Task-oriented Dialogue System

Code for the ICCV2021 paper "Personalized Image Semantic Segmentation"

Submission to Twitter's algorithmic bias bounty challenge

✅ How Robust are Fact Checking Systems on Colloquial Claims?. In NAACL-HLT, 2021.

MinHash, LSH, LSH Forest, Weighted MinHash, HyperLogLog, HyperLogLog++, LSH Ensemble

DiAne is a smart fuzzer for IoT devices

Action Segmentation Evaluation