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

Turi Create simplifies the development of custom machine learning models.

FedCV: A Federated Learning Framework for Diverse Computer Vision Tasks

OpenMMLab Computer Vision Foundation

Dynamical Wasserstein Barycenters for Time Series Modeling

Neural Scene Flow Prior (NeurIPS 2021 spotlight)

YoloAll is a collection of yolo all versions. you you use YoloAll to test yolov3/yolov5/yolox/yolo_fastest

Implementation of ConvMixer for "Patches Are All You Need? 🤷"

DeepSTD: Mining Spatio-temporal Disturbances of Multiple Context Factors for Citywide Traffic Flow Prediction

PyTorch-LIT is the Lite Inference Toolkit (LIT) for PyTorch which focuses on easy and fast inference of large models on end-devices.

An official reimplementation of the method described in the INTERSPEECH 2021 paper - Speech Resynthesis from Discrete Disentangled Self-Supervised Representations.

CasualHealthcare's Pneumonia detection with Artificial Intelligence (Convolutional Neural Network)

BookMyShowPC - Movie Ticket Reservation App made with Tkinter

GT China coal model

Extreme Rotation Estimation using Dense Correlation Volumes

[CVPR 2022 Oral] Versatile Multi-Modal Pre-Training for Human-Centric Perception

Pseudo-mask Matters in Weakly-supervised Semantic Segmentation

Autoencoder - Reducing the Dimensionality of Data with Neural Network

Simultaneous Detection and Segmentation

This is a tensorflow-based rotation detection benchmark, also called AlphaRotate.

SatelliteSfM - A library for solving the satellite structure from motion problem