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
Supplementary Fig. 7	link	path
Supplementary Fig. 8	link	path
Supplementary Fig. 9	link	path
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

An LSTM based GAN for Human motion synthesis

A Multi-modal Perception Tracker (MPT) for speaker tracking using both audio and visual modalities

It is a simple library to speed up CLIP inference up to 3x (K80 GPU)

FlowTorch is a PyTorch library for learning and sampling from complex probability distributions using a class of methods called Normalizing Flows

Eff video representation - Efficient video representation through neural fields

Source code for "Progressive Transformers for End-to-End Sign Language Production" (ECCV 2020)

A PyTorch implementation of ViTGAN based on paper ViTGAN: Training GANs with Vision Transformers.

Deep Crop Rotation

Defending graph neural networks against adversarial attacks (NeurIPS 2020)

Use VITS and Opencpop to develop singing voice synthesis; Maybe it will VISinger.

Keeping it safe - AI Based COVID-19 Tracker using Deep Learning and facial recognition

This is a repository of our model for weakly-supervised video dense anticipation.

Projects of Andfun Yangon

Localization Distillation for Object Detection

Seeing if I can put together an interactive version of 3b1b's Manim in Streamlit

A pre-trained language model for social media text in Spanish

CATE: Computation-aware Neural Architecture Encoding with Transformers

Tensorforce: a TensorFlow library for applied reinforcement learning

Flickr-Faces-HQ (FFHQ) is a high-quality image dataset of human faces, originally created as a benchmark for generative adversarial networks (GAN)

Use deep learning, genetic programming and other methods to predict stock and market movements