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
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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

QR2Pass-project - A proof of concept for an alternative (passwordless) authentication system to a web server

这是一个mobilenet-yolov4-lite的库，把yolov4主干网络修改成了mobilenet，修改了Panet的卷积组成，使参数量大幅度缩小。

A modular domain adaptation library written in PyTorch.

PyTorch implementation of DeepLab v2 on COCO-Stuff / PASCAL VOC

Implementations of polygamma, lgamma, and beta functions for PyTorch

Distributed Arcface Training in Pytorch

Selective Wavelet Attention Learning for Single Image Deraining

HiPAL: A Deep Framework for Physician Burnout Prediction Using Activity Logs in Electronic Health Records

Implementation of Continuous Sparsification, a method for pruning and ticket search in deep networks

Learning an Adaptive Meta Model-Generator for Incrementally Updating Recommender Systems

Towards Open-World Feature Extrapolation: An Inductive Graph Learning Approach

Python framework for Stochastic Differential Equations modeling

ACL'2021: LM-BFF: Better Few-shot Fine-tuning of Language Models

Code and data form the paper BERT Got a Date: Introducing Transformers to Temporal Tagging

Augmented Traffic Control: A tool to simulate network conditions

Molecular AutoEncoder in PyTorch

Calling Julia from Python - an experiment on data loading

Contextual Attention Network: Transformer Meets U-Net

UltraGCN: An Ultra Simplification of Graph Convolutional Networks for Recommendation

[CVPR 2022] Official Pytorch code for OW-DETR: Open-world Detection Transformer