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

MINIROCKET: A Very Fast (Almost) Deterministic Transform for Time Series Classification

Retinal vessel segmentation based on GT-UNet

AdaDM: Enabling Normalization for Image Super-Resolution

Cognition-aware Cognate Detection

Official implementation of particle-based models (GNS and DPI-Net) on the Physion dataset.

Multi-Modal Fingerprint Presentation Attack Detection: Evaluation On A New Dataset

CVNets: A library for training computer vision networks

PartImageNet is a large, high-quality dataset with part segmentation annotations

Jittor 64*64 implementation of StyleGAN

Next-gen Rowhammer fuzzer that uses non-uniform, frequency-based patterns.

working repo for my xumx-sliCQ submissions to the ISMIR 2021 MDX

ProjectOxford-ClientSDK - This repo has moved :house: Visit our website for the latest SDKs & Samples

render sprites into your desktop environment as shaped windows using GTK

[ArXiv 2021] Data-Efficient Instance Generation from Instance Discrimination

Alias-Free Generative Adversarial Networks (StyleGAN3) Official PyTorch implementation

[ICCV 2021 Oral] Mining Latent Classes for Few-shot Segmentation

Random Erasing Data Augmentation. Experiments on CIFAR10, CIFAR100 and Fashion-MNIST

Instance-conditional Knowledge Distillation for Object Detection

Optimizes image files by converting them to webp while also updating all references.

An implementation of a sequence to sequence neural network using an encoder-decoder