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
Extended Data Fig. 4	link	path
Extended Data Fig. 5	link	path
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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. 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 hidden low dimensional dyanmics using a Generalized Onsager Principle and neural networks

[ICCV 2021] Official Pytorch implementation for Discriminative Region-based Multi-Label Zero-Shot Learning SOTA results on NUS-WIDE and OpenImages

Unofficial reimplementation of ECAPA-TDNN for speaker recognition (EER=0.86 for Vox1_O when train only in Vox2)

CMUA-Watermark: A Cross-Model Universal Adversarial Watermark for Combating Deepfakes (AAAI2022)

A PyTorch implementation of NeRF (Neural Radiance Fields) that reproduces the results.

This application is the basic of automated online-class-joiner(for YıldızEdu) within the right time. Gets the ZOOM link by scheduled date and time.

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

OpenIPDM is a MATLAB open-source platform that stands for infrastructures probabilistic deterioration model

We will see a basic program that is basically a hint to brute force attack to crack passwords. In other words, we will make a program to Crack Any Password Using Python. Show some ❤️ by starring this repository!

Source code for "OmniPhotos: Casual 360° VR Photography"

📚 Papermill is a tool for parameterizing, executing, and analyzing Jupyter Notebooks.

Edge-aware Guidance Fusion Network for RGB-Thermal Scene Parsing

[3DV 2021] Channel-Wise Attention-Based Network for Self-Supervised Monocular Depth Estimation

PyTorch implementation of "Image-to-Image Translation Using Conditional Adversarial Networks".

Forecasting with Gradient Boosted Time Series Decomposition

Semantic Segmentation Architectures Implemented in PyTorch

An addon uses SMPL's poses and global translation to drive cartoon character in Blender.

Codebase to experiment with a hybrid Transformer that combines conditional sequence generation with regression

Code for Estimating Multi-cause Treatment Effects via Single-cause Perturbation (NeurIPS 2021)

This is the repo of the manuscript "Dual-branch Attention-In-Attention Transformer for speech enhancement"