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)
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Supplementary Figures

Figure	nbviewer	Notebook Path
Supplementary Fig. 1	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

Learning to trade under the reinforcement learning framework

MoViNets PyTorch implementation: Mobile Video Networks for Efficient Video Recognition;

Testing and Estimation of structural breaks in Stata

ManiSkill-Learn is a framework for training agents on SAPIEN Open-Source Manipulation Skill Challenge (ManiSkill Challenge), a large-scale learning-from-demonstrations benchmark for object manipulation.

ArtEmis: Affective Language for Art

Pytorch cuda extension of grid_sample1d

Codebase for arXiv preprint "NeRF++: Analyzing and Improving Neural Radiance Fields"

PyTorch evaluation code for Delving Deep into the Generalization of Vision Transformers under Distribution Shifts.

A python program to hack instagram

Code for our paper "Multi-scale Guided Attention for Medical Image Segmentation"

Generic image compressor for machine learning. Pytorch code for our paper "Lossy compression for lossless prediction".

Unofficial PyTorch code for BasicVSR

PyTorch implementation of PP-LCNet

A minimalist environment for decision-making in autonomous driving

A Python Library for Graph Outlier Detection (Anomaly Detection)

A Pytorch Implementation of Domain adaptation of object detector using scissor-like networks

Storage-optimizer - Identify potintial optimizations on the cloud storage accounts

an implementation of softmax splatting for differentiable forward warping using PyTorch

EEGEyeNet is benchmark to evaluate ET prediction based on EEG measurements with an increasing level of difficulty

Evaluating saliency methods on artificial data with different background types