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/
Converts a base copy of Pokemon BDSP's masterdatas into a more readable and editable Pokemon Showdown Format.

Showdown-BDSP-Converter Converts a base copy of Pokemon BDSP's masterdatas into a more readable and editable Pokemon Showdown Format. Download the lat

Alden Mo 2 Jan 02, 2022
A simple armature retargeting tool for Blender

Simple-Retarget-Tool-Blender A simple armature retargeting tool for Blender Update V2: Set Rest Pose to easily apply rest pose. Preset Import/Export.

Fahad Hasan Pathik 74 Jan 04, 2023
This is an independent project to track Nubank expenses

Nubank expense tracker This is an independent project to track Nubank expenses. To fetch Nubank data we are going to use an unofficial Nubank API, tha

Ramon Gazoni Lacerda 0 Aug 28, 2022
Data Science Course at Dept. of Computer Engineering, Chula 2022

2110446 Data Science Course at Chula 2022 Short links for exercises: Week1: Intro to Numpy, Pandas Numpy: https://colab.research.google.com/github/kao

Kao Panboonyuen 17 Nov 27, 2022
Streamlit component to display topics from Streamlit's community forum related to any exception.

streamlit-forum Streamlit component to display topics from Streamlit's community forum related to any exception. Installation pip install streamlit-fo

Snehan Kekre 7 Jul 15, 2022
Python script to commit to your github for a perfect commit streak. This is purely for education purposes, please don't use this script to do bad stuff.

Daily-Git-Commit Commit to repo every day for the perfect commit streak Requirments pip install -r requirements.txt Setup Download this repository. Cr

JareBear 34 Dec 14, 2022
It's like Forth but in Python

It's like Forth but written in Python. But I don't actually know for sure since I never programmed in Forth, I only heard that it's some sort of stack-based programming language. Porth is also stack-

Tsoding 619 Dec 21, 2022
Spooky Castle Project

Spooky Castle Project Here is a repository where I have placed a few workflow scripts that could be used to automate the blender to godot sprite pipel

3 Jan 17, 2022
A streaming animation of all the edits to a given Wikipedia page.

WikiFilms! What is it? A streaming animation of all the edits to a given Wikipedia page. How it works. It works by creating a "virtual camera," which

Tal Zaken 2 Jan 18, 2022
Extrator de dados do jupiterweb

Extrator de dados do jupiterweb O programa é composto de dois arquivos: Um constando apenas de classes complementares que representam as unidades e as

Bruno Aricó 2 Nov 28, 2022
Gerenciador de processos e registros pessoais do Departamento de Fiscalização de Produtos Controlados.

CRManager Gerenciador de processos e registros pessoais do Departamento de Fiscalização de Produtos Controlados. Descrição Este projeto tem como objet

Wolfgang Almeida 1 Nov 15, 2021
This is an online course where you can learn and master the skill of low-level performance analysis and tuning.

Performance Ninja Class This is an online course where you can learn to find and fix low-level performance issues, for example CPU cache misses and br

Denis Bakhvalov 1.2k Dec 30, 2022
Transform a Google Drive server into a VFX pipeline ready server

Google Drive VFX Server VFX Pipeline About The Project Quick tutorial to setup a Google Drive Server for multiple machines access, and VFX Pipeline on

Valentin Beaumont 17 Jun 27, 2022
A full-featured, hackable tiling window manager written and configured in Python

A full-featured, hackable tiling window manager written and configured in Python Features Simple, small and extensible. It's easy to write your own la

Qtile 3.8k Dec 31, 2022
Personal Assistant Tessa

Personal Assistant Tessa Introducing our all new personal assistant Tessa..... An intelligent virtual assistant (IVA) or intelligent personal assistan

Anusha Joseph 4 Mar 08, 2022
NFT generator for Solana!

Solseum NFT Generator for Solana! Check this guide here! Creating your randomized uniques NFTs, getting rarity information and displaying it on a webp

Solseum™ VR NFTs 145 Dec 30, 2022
Demo code for "Logs in distributed systems" webinar

Hexlet Logs Demo Пререквизиты docker-compose python3 Учетка в DataDog Базовое понимание, что такое логи (можно почитать гайд

Anton Markelov 1 Dec 01, 2021
The only purpose of a byte-sized application is to help you create .desktop entry files for downloaded applications.

Turtle 🐢 The only purpose of a byte-sized application is to help you create .desktop entry files for downloaded applications. As of usual with elemen

TenderOwl 14 Dec 29, 2022
validation for pre-commit.ci configuration

pre-commit-ci-config validation for pre-commit.ci configuration installation pip install pre-commit-ci-config api pre_commit_ci_config.SCHEMA a cfgv s

pre-commit.ci 17 Jul 11, 2022
A toy repo illustrating a minimal installable Python package

MyToy: a minimal Python package This repository contains a minimal, toy Python package with a few files as illustration for students of how to lay out

Fernando Perez 19 Apr 24, 2022