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

Learning to Map Large-scale Sparse Graphs on Memristive Crossbar

Leveraging Instance-, Image- and Dataset-Level Information for Weakly Supervised Instance Segmentation

A fast python implementation of Ray Tracing in One Weekend using python and Taichi

Official implementation of Deep Convolutional Dictionary Learning for Image Denoising.

Implement of homography net by pytorch

Official implementation of UTNet: A Hybrid Transformer Architecture for Medical Image Segmentation

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

Codes for the compilation and visualization examples to the HIF vegetation dataset

Convert game ISO and archives to CD CHD for emulation on Linux.

TigerLily: Finding drug interactions in silico with the Graph.

Analysis of Smiles through reservoir sampling & RDkit

A Python module for parallel optimization of expensive black-box functions

Automatic differentiation with weighted finite-state transducers.

CaFM-pytorch ICCV ACCEPT Introduction of dataset VSD4K

The implementation of the algorithm in the paper "Safe Deep Semi-Supervised Learning for Unseen-Class Unlabeled Data" published in ICML 2020.

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

A Pytorch Implementation of a continuously rate adjustable learned image compression framework.

This is a five-step framework for the development of intrusion detection systems (IDS) using machine learning (ML) considering model realization, and performance evaluation.

Code for KiloNeRF: Speeding up Neural Radiance Fields with Thousands of Tiny MLPs

Breaking Shortcut: Exploring Fully Convolutional Cycle-Consistency for Video Correspondence Learning