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

Scheduling BilinearRewards

Pytorch Implementation of Interaction Networks for Learning about Objects, Relations and Physics

[ICCV 2021] Excavating the Potential Capacity of Self-Supervised Monocular Depth Estimation

How the Deep Q-learning method works and discuss the new ideas that makes the algorithm work

[ICCV 2021 Oral] PoinTr: Diverse Point Cloud Completion with Geometry-Aware Transformers

Deep ViT Features as Dense Visual Descriptors

Leveraging Instance-, Image- and Dataset-Level Information for Weakly Supervised Instance Segmentation

LF-YOLO (Lighter and Faster YOLO) is used to detect defect of X-ray weld image.

Python code for the paper How to scale hyperparameters for quickshift image segmentation

Python3 Implementation of (Subspace Constrained) Mean Shift Algorithm in Euclidean and Directional Product Spaces

"Domain Adaptive Semantic Segmentation without Source Data" (ACM MM 2021)

TANL: Structured Prediction as Translation between Augmented Natural Languages

nextPARS, a novel Illumina-based implementation of in-vitro parallel probing of RNA structures.

PyTorch implementation of NIPS 2017 paper Dynamic Routing Between Capsules

Towards the D-Optimal Online Experiment Design for Recommender Selection (KDD 2021)

Code for "Learning to Segment Rigid Motions from Two Frames".

Monocular Depth Estimation Using Laplacian Pyramid-Based Depth Residuals

Fight Recognition from Still Images in the Wild @ WACVW2022, Real-world Surveillance Workshop

Its a Plant Leaf Disease Detection System based on Machine Learning.

Adversarial Reweighting for Partial Domain Adaptation