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

Probabilistic Cross-Modal Embedding (PCME) CVPR 2021

People Interaction Graph

Task-related Saliency Network For Few-shot learning

A sequence of Jupyter notebooks featuring the 12 Steps to Navier-Stokes

[ICCV 2021] Code release for "Sub-bit Neural Networks: Learning to Compress and Accelerate Binary Neural Networks"

Official PyTorch implementation of "Improving Face Recognition with Large AgeGaps by Learning to Distinguish Children" (BMVC 2021)

The code for our paper submitted to RAL/IROS 2022: OverlapTransformer: An Efficient and Rotation-Invariant Transformer Network for LiDAR-Based Place Recognition.

Learned image compression

Tensorflow2.0 🍎🍊 is delicious, just eat it! 😋😋

A repository for storing njxzc final exam review material

This is a Keras-based Python implementation of DeepMask- a complex deep neural network for learning object segmentation masks

Graph Representation Learning via Graphical Mutual Information Maximization

ESGD-M - A stochastic non-convex second order optimizer, suitable for training deep learning models, for PyTorch

Intel® Neural Compressor is an open-source Python library running on Intel CPUs and GPUs

1st place solution in CCF BDCI 2021 ULSEG challenge

A particular navigation route using satellite feed and can help in toll operations & traffic managemen

Differentiable Quantum Chemistry (only Differentiable Density Functional Theory and Hartree Fock at the moment)

Bling's Object detection tool

Official code for paper "ISNet: Costless and Implicit Image Segmentation for Deep Classifiers, with Application in COVID-19 Detection"

Scaling and Benchmarking Self-Supervised Visual Representation Learning