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
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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

ivadomed is an integrated framework for medical image analysis with deep learning.

Creating Artificial Life with Reinforcement Learning

Charsiu: A transformer-based phonetic aligner

Most popular metrics used to evaluate object detection algorithms.

PyTorch implementation for OCT-GAN Neural ODE-based Conditional Tabular GANs (WWW 2021)

Official PyTorch implementation of GDWCT (CVPR 2019, oral)

Implementation of SSMF: Shifting Seasonal Matrix Factorization

CSAW-M: An Ordinal Classification Dataset for Benchmarking Mammographic Masking of Cancer

A Pytorch Implementation of [Source data‐free domain adaptation of object detector through domain

Libraries, tools and tasks created and used at DeepMind Robotics.

Text and code for the forthcoming second edition of Think Bayes, by Allen Downey.

The code repository for "PyCIL: A Python Toolbox for Class-Incremental Learning" in PyTorch.

ViSER: Video-Specific Surface Embeddings for Articulated 3D Shape Reconstruction

This is an official implementation for "DeciWatch: A Simple Baseline for 10x Efficient 2D and 3D Pose Estimation"

Source code for Fixed-Point GAN for Cloud Detection

The official implementation of paper Siamese Transformer Pyramid Networks for Real-Time UAV Tracking, accepted by WACV22

Raptor-Multi-Tool - Raptor Multi Tool With Python

Official code release for 3DV 2021 paper Human Performance Capture from Monocular Video in the Wild.

Detect roadway lanes using Python OpenCV for project during the 5th semester at DHBW Stuttgart for lecture in digital image processing.

Interactive dimensionality reduction for large datasets