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
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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

Implementation of the paper "Shapley Explanation Networks"

Projects for AI/ML and IoT integration for games and other presented at re:Invent 2021.

🍀 Pytorch implementation of various Attention Mechanisms, MLP, Re-parameter, Convolution, which is helpful to further understand papers.⭐⭐⭐

Code for our method RePRI for Few-Shot Segmentation. Paper at http://arxiv.org/abs/2012.06166

A PyTorch Implementation of Single Shot Scale-invariant Face Detector.

An original implementation of "MetaICL Learning to Learn In Context" by Sewon Min, Mike Lewis, Luke Zettlemoyer and Hannaneh Hajishirzi

This repository is for Competition for ML_data class

A PyTorch implementation of the Relational Graph Convolutional Network (RGCN).

Course materials for Fall 2021 "CIS6930 Topics in Computing for Data Science" at New College of Florida

Catch-all collection of generative art made using processing

A modern pure-Python library for reading PDF files

Use tensorflow to implement a Deep Neural Network for real time lane detection

Semantically Contrastive Learning for Low-light Image Enhancement

This is a project based on retinaface face detection, including ghostnet and mobilenetv3

Code release for NeRF (Neural Radiance Fields)

Table-Extractor 表格抽取

PyTorch implementation of paper "StarEnhancer: Learning Real-Time and Style-Aware Image Enhancement" (ICCV 2021 Oral)

Nightmare-Writeup - Writeup for the Nightmare CTF Challenge from 2022 DiceCTF

Robustness via Cross-Domain Ensembles

A multilingual version of MS MARCO passage ranking dataset