Test reproducibility of leiden/umap on different systems

Related tags

Miscellaneousscanpy_reproducibility
Overview

Test reproducibility of leiden/umap on different systems

This nextflow pipeline runs a jupyter notebook that runs

sc.pp.neighbors
sc.tl.umap
sc.tl.leiden

on a test dataset with a pre-computed latent representation stored in adata.obsm["X_scVI"].

The test-dataset is available in the data directory.

Running the pipeline

There are a few minor things you may need to adjust on your system:

  • The run_pipeline.sh script starts nextflow with a work directory and a profile specific to our institute.
  • The clusterOptions is used to submit the jobs to different nodes on our HPC and is specific to our queue and node names.
  • The node names are passed on to clusterOptions from a channel defined in main.nf.

Results

The results (tested on 5 nodes, 4 of which have different CPUs) are available from: https://grst.github.io/scanpy_reproducibility/

You might also like...
Python wrapper to different clients to determine how a particular term is used.

Python wrapper to different clients to determine how a particular term is used.

Chris Mungall 3 Oct 24, 2022
Leveraging pythonic forces to defeat different coding challenges 🐍
Leveraging pythonic forces to defeat different coding challenges 🐍

Pyforces Leveraging pythonic forces to defeat different coding challenges! Table of Contents Pyforces Tests Pyforces Pyforces is a study repo with a c

Igor Grillo Peternella 8 Dec 14, 2022
This is some simple code to scrape vistbook's system to get an overview of the different cabins availability.

DNT_cabin_availability_system This is some simple code to scrape visbook's system to get an overview of the different cabins availability. The system

Andreas Lorentzen 1 Sep 25, 2022
Moji sends text and fun facts from different APIs wit da use of a notification deamon
Moji sends text and fun facts from different APIs wit da use of a notification deamon

Moji sends text and fun facts from different APIs wit da use of a notification deamon. Can be runned via dmenu or rofi.

kshly 2 Jan 12, 2022
News-app - This is a news web app for reading news from different sources and topics
News-app - This is a news web app for reading news from different sources and topics

News-app - This is a news web app for reading news from different sources and topics

null 1 Feb 2, 2022
Different steganography methods with examples and my own small image database

literally-the-most-useless-project [Different steganography methods with examples and my own small image database] This project currently contains thr

Kamyishka 1 Dec 9, 2022
Structural basis for solubility in protein expression systems

Structural basis for solubility in protein expression systems Large-scale protein production for biotechnology and biopharmaceutical applications rely

ProteinQure 16 Aug 18, 2022
LSO, also known as Linux Swap Operator, is a software with both GUI and terminal versions that you can manage the Swap area for Linux operating systems.
LSO, also known as Linux Swap Operator, is a software with both GUI and terminal versions that you can manage the Swap area for Linux operating systems.

LSO - Linux Swap Operator Türkçe - LSO Nedir? LSO, diğer adıyla Linux Swap Operator Linux işletim sistemleri için Swap alanını yönetebileceğiniz hem G

Eren İnce 4 Feb 9, 2022
ASVspoof 2021 Baseline Systems

ASVspoof 2021 Baseline Systems Baseline systems are grouped by task: Speech Deepfake (DF) Logical Access (LA) Physical Access (PA) Please find more de

null 91 Dec 28, 2022
Comments
  • Inquiry: any explanations?

    Inquiry: any explanations?

    Hello,

    I observed exactly the same thing as you showed in the demonstration, when it differs, the global structure in 2D UMAP seems similar but there will be displacements in each specific region.

    I was wondering, would you happen to have some explanations for that? Since the randomness should have been controlled by specifying the seed.

    Thanks, Frank

    opened by frankligy 1
Releases(containers-0.1.0)
Owner
Gregor Sturm
Always stay curious!
Gregor Sturm
GitHub Repository https://grst.github.io/scanpy_reproducibility/
Airplane reservation system python 2

airplane-reservation-system-python-2 Announcement 🔊 : 🔴 IMPORTANT 🔴 : Few new things have been added into the code [16/05/2021] different names is

voyager2005 1 Dec 06, 2021
《practical python programming》的中文翻译

欢迎光临 大约 25 年前，当我第一次学习 Python 时，发现 Python 竟然可以被高效地应用到各种混乱的工作项目上，我立即被震惊了。15 年前，我自己也将这种乐趣教授给别人。教学的结果就是本课程——一门实用的学习 Python的课程。

编程人 125 Dec 17, 2022
WhyNotWin11 - Detection Script to help identify why your PC isn't Windows 11 Release Ready

WhyNotWin11 - Detection Script to help identify why your PC isn't Windows 11 Release Ready

Robert C. Maehl 5.9k Dec 31, 2022
Set named timers for cooking, watering plants, brewing tea and more.

Timer Set named timers for cooking, watering plants, brewing tea and more. About Use Mycroft when your hands are messy or you need more that the one t

OpenVoiceOS 3 Nov 02, 2022
Vector tile server for the Wildfire Predictive Services Unit

wps-tileserver Vector tile server for the Wildfire Predictive Services Unit Overview The intention of this project is to: provide tools to easily spin

Province of British Columbia 6 Dec 20, 2022
JSEngine is a simple wrapper of Javascript engines.

JSEngine This is a simple wrapper of Javascript engines, it wraps the Javascript interpreter for Python use. There are two ways to call interpreters,

11 Dec 18, 2022
Python decorator for `TODO`s

Python decorator for `TODO`s. Don't let your TODOs rot in your python projects anymore !

Klemen Sever 74 Sep 13, 2022
Site de gestion de cave à vin utilisant une BDD manipulée avec SQLite3 via Python

cave-vin Site de gestion de cave à vin utilisant une bdd manipulée avec MySQL ACCEDER AU SITE : Pour accéder à votre cave vous aurez besoin de lancer

Elouann Lucas 0 Jul 05, 2022
Python with the scientific stack, compiled to WebAssembly.

Pyodide may be used in any context where you want to run Python inside a web browser.

9.5k Jan 09, 2023
Create N Share is a No Code solution which gives users the ability to create any type of feature rich survey forms with ease.

create n share Note : The Project Scaffold will be pushed soon. Create N Share is a No Code solution which gives users the ability to create any type

Chiraag Kakar 11 Dec 03, 2022
A student information management system in Python

Student-information-management-system 本项目是一个学生信息管理系统，这个项目是用Python语言实现的，也实现了图形化界面的显示，同时也实现了管理员端，学生端两个登陆入口，同时底层使用的是Redis做的数据持久化。 This project is a stude

liuyunfei 7 Nov 15, 2022
Online HackerRank problem solving challenges

LinkedListHackerRank Online HackerRank problem solving challenges This challenge is part of a tutorial track by MyCodeSchool You are given the pointer

Sefineh Tesfa 1 Nov 21, 2021
Reconhecimento de voz, em português, com python

Speech_recognizer Reconhecimento de voz, em português, com python O ato de falar nada mais é que criar vibrações no ar. Por meio de um conversor analó

Marcus Vinícius Ribeiro Andrade 1 Dec 14, 2021
Xbps-install wrapper written in Python that doesn't care about case sensitiveness and package versions

xbi Xbps-install wrapper written in Python that doesn't care about case sensitiveness and package versions. Description This Python script can be easi

Emanuele Sabato 5 Apr 11, 2022
This directory gathers the tools developed by the Data Sourcing Working Group

BigScience Data Sourcing Code This directory gathers the tools developed by the Data Sourcing Working Group First Sourcing Sprint: October 2021 The co

BigScience Workshop 27 Nov 04, 2022
Find virtual hosts (vhosts) from IP addresses and hostnames

Features Enumerate vhosts from a list of IP addresses and domain names. Virtual Hosts are enumerated using the following process: Supplied domains are

3 Jul 09, 2022
Weakly-Divisable - Takes an interger and seee if it is weakly divisible by seven

Weakly Divisble Project by Diana Arce-Hernandez, Ryan McAlpine, and Rommel Ravan

Diana Arce-Hernandez 1 Jan 12, 2022
This tool for beginner and help those people they gather information about Email Header Analysis, Instagram Information, Instagram Username Check, Ip Information, Phone Number Information, Port Scan

This tool for beginner and help those people they gather information about Email Header Analysis, Instagram Information, Instagram Username Check, Ip Information, Phone Number Information, Port Scan.

cb-kali 5 Feb 18, 2022
A Notifier Program that Notifies you to relax your eyes Every 15 Minutes👀

Every 15 Minutes is an application that is used to Notify you to Relax your eyes Every 15 Minutes, This is fully made with Python and also with the us

Ashely Sato 1 Nov 02, 2021
Demo scripts for the Kubernetes Security Webinar

Kubernetes Security Webinar [in Russian] YouTube video (October 13, 2021) Authors: Artem Yushkovsky (LinkedIn, GitHub) Maxim Mosharov @ Whitespots.io

Slurm 34 Dec 06, 2022