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

Official PyTorch implementation of StyleGAN3

SCALE: Modeling Clothed Humans with a Surface Codec of Articulated Local Elements (CVPR 2021)

AlgoVision - A Framework for Differentiable Algorithms and Algorithmic Supervision

Fast methods to work with hydro- and topography data in pure Python.

Continuous Conditional Random Field Convolution for Point Cloud Segmentation

Readings for "A Unified View of Relational Deep Learning for Polypharmacy Side Effect, Combination Therapy, and Drug-Drug Interaction Prediction."

RDA: Robust Domain Adaptation via Fourier Adversarial Attacking

Cervix ROI Segmentation Using U-NET

Sample and Computation Redistribution for Efficient Face Detection

Motion Planner Augmented Reinforcement Learning for Robot Manipulation in Obstructed Environments (CoRL 2020)

Source codes for "Structure-Aware Abstractive Conversation Summarization via Discourse and Action Graphs"

SMPLpix: Neural Avatars from 3D Human Models

This repo contains the official implementations of EigenDamage: Structured Pruning in the Kronecker-Factored Eigenbasis

Code repository for "Reducing Underflow in Mixed Precision Training by Gradient Scaling" presented at IJCAI '20

SPCL: A New Framework for Domain Adaptive Semantic Segmentation via Semantic Prototype-based Contrastive Learning

Drone detection using YOLOv5

Implementation of "Bidirectional Projection Network for Cross Dimension Scene Understanding" CVPR 2021 (Oral)

Deconfounding Temporal Autoencoder: Estimating Treatment Effects over Time Using Noisy Proxies

Repository of 3D Object Detection with Pointformer (CVPR2021)

tmm_fast is a lightweight package to speed up optical planar multilayer thin-film device computation.