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
Supplementary Fig. 6	link	path
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Supplementary Fig. 10	link	path
Supplementary Fig. 11	link	path
Supplementary Fig. 12	link1 link2	path1 path2
Supplementary Fig. 13	link	path
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

FAVD: Featherweight Assisted Vulnerability Discovery

Easily pull telemetry data and create beautiful visualizations for analysis.

A reimplementation of DCGAN in PyTorch

Implementation of the method proposed in the paper "Neural Descriptor Fields: SE(3)-Equivariant Object Representations for Manipulation"

Attempt at implementation of a simple GAN using Keras

The missing CMake project initializer

Exploiting Robust Unsupervised Video Person Re-identification

PyTorch implementation of the ExORL: Exploratory Data for Offline Reinforcement Learning

SoGCN: Second-Order Graph Convolutional Networks

Public scripts, services, and configuration for running a smart home K3S network cluster

App customer segmentation cohort rfm clustering

AI that generate music

TabNet for fastai

This tool converts a Nondeterministic Finite Automata (NFA) into a Deterministic Finite Automata (DFA)

Complete the code of prefix-tuning in low data setting

Training Cifar-10 Classifier Using VGG16

Train Yolov4 using NBX-Jobs

Tom-the-AI - A compound artificial intelligence software for Linux systems.

My published benchmark for a Kaggle Simulations Competition

Implementation of Bottleneck Transformer in Pytorch