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
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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

O2O-Afford: Annotation-Free Large-Scale Object-Object Affordance Learning (CoRL 2021)

This is the code used in the paper "Entity Embeddings of Categorical Variables".

Robust Self-augmentation for NER with Meta-reweighting

Learning from History: Modeling Temporal Knowledge Graphs with Sequential Copy-Generation Networks

Implementation of Memory-Efficient Neural Networks with Multi-Level Generation, ICCV 2021

Codes for NAACL 2021 Paper "Unsupervised Multi-hop Question Answering by Question Generation"

Implementation of NÜWA, state of the art attention network for text to video synthesis, in Pytorch

Record radiologists' eye gaze when they are labeling images.

Self-Supervised Deep Blind Video Super-Resolution

Editing a Conditional Radiance Field

Adversarial-Information-Bottleneck - Distilling Robust and Non-Robust Features in Adversarial Examples by Information Bottleneck (NeurIPS21)

Deep learning library featuring a higher-level API for TensorFlow.

The code is an implementation of Feedback Convolutional Neural Network for Visual Localization and Segmentation.

Official codebase for running the small, filtered-data GLIDE model from GLIDE: Towards Photorealistic Image Generation and Editing with Text-Guided Diffusion Models.

Image classification for projects and researches

Revitalizing CNN Attention via Transformers in Self-Supervised Visual Representation Learning

Context-Sensitive Misspelling Correction of Clinical Text via Conditional Independence, CHIL 2022

GoodNews Everyone! Context driven entity aware captioning for news images

The repository offers the official implementation of our BMVC 2021 paper in PyTorch.

Code repository for our paper regarding the L3D dataset.