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/
dotfiles - Cristian Valero Abundio

In this repository you can find various configurations to configure your Linux operating system, preferably ArchLinux and its derivatives.

Cristian Valero Abundio 1 Jan 09, 2022
The git for the Python Story Utility Package library.

PSUP, The Python Story Utility Package Module. PSUP helps making stories or games with options, diverging paths, different endings and so on. You can

Enoki 6 Nov 27, 2022
An example file showing a simple endpoints like a login/logout function and maybe some others.

Flask API Example An example project showing a simple endpoints like a login/logout function and maybe some others. How to use: Open up your IDE (or u

Kevin 1 Oct 27, 2021
Skip spotify ads by automatically restarting application when ad comes

SpotiByeAds No one likes interruptions! Don't you hate it when you're listening to your favorite jazz track or your EDM playlist and an ad for Old Spi

Partho 287 Dec 29, 2022
Google Scholar App Using Python

Google Scholar App Watch the tutorial video How to build a Google Scholar App | Streamlit #30 Demo Launch the web app: Reproducing this web app To rec

Chanin Nantasenamat 4 Jun 05, 2022
Automated rop chain generation

This is the accompanying code to the blog post talking about automated rop chain generation. Build the test file with: make Install the dependencies:

Christopher Roberts 14 Nov 22, 2022
WildHack 2021 solution by Nuclear Foxes team (public version).

WildHack 2021 Nuclear Foxes Team This repo contains our project for the Wildberries Hackathon 2021. Task 2: Searching tags Implement an algorithm of r

Sergey Zakharov 1 Apr 18, 2022
Easily Generate Revolut Business Cards

RevBusinessCardGen Easily Generate Revolut Business Cards Prerequisites Before you begin, ensure you have met the following requirements: You have ins

Younes™ 35 Dec 14, 2022
List of Linux Tools I put on almost every linux / Debian host

Linux-Tools List of Linux Tools I put on almost every Linux / Debian host Installed: geany -- GUI editor/ notepad++ like chkservice -- TUI Linux ser

Stew Alexander 20 Jan 02, 2023
DD监控室第一版

DD监控室 运行指南

执明神君 1.2k Dec 31, 2022
A simple but fully functional calculator that will take multiple operations.

Functional-Calculator A simple but fully functional calculator that will take multiple operations. Usage Run the following command through terminal: p

Uzziel Ariel 1 Dec 22, 2022
200 LeetCode problems

LeetCode I classify 200 leetcode problems into some categories and upload my code to who concern WEEK 1 # Title Difficulty Array 15 3Sum Medium 1324 P

Hoang Cao Bao 108 Dec 08, 2022
Logo DYS (Doküman Yönetim Sitemi) API Python Implementation

dys-connector Logo DYS (Dokuman Yonetim Sistemi) API Python Implementation Python Package: https://pypi.org/project/dys-connector Quick Start from dys

Logo Group 8 Mar 19, 2022
BinCat is an innovative login system, with which the account you register will be more secure.

BinCat is an innovative login system, with which the account you register will be more secure. This project is inspired by a conventional token system.

Hipotesi 2 May 22, 2022
a simple functional programming language compiler written in python

Functional Programming Language A compiler for my small functional language. Written in python with SLY lexer/parser generator library. Requirements p

Ashkan Laei 3 Nov 05, 2021
OpenTable Reservation Maker For Python

OpenTable-Reservation-Maker The code that corresponds with this blog post on writing a script to make reservations for me on opentable Getting started

JonLuca De Caro 36 Nov 10, 2022
Library for Memory Trace Statistics in Python

Memory Search Library for Memory Trace Statistics in Python The library uses tracemalloc as a core module, which is why it is only available for Pytho

Memory Search 1 Dec 20, 2021
ColabFold / AlphaFold2_advanced on your local PC (or macOS)

LocalColabFold ColabFold / AlphaFold2_advanced on your local PC (or macOS) Installation For Linux Make sure curl and wget commands are already install

Yoshitaka Moriwaki 207 Dec 22, 2022
Modern API wrapper for Genshin Impact built on asyncio and pydantic.

genshin.py Modern API wrapper for Genshin Impact built on asyncio and pydantic.

sadru 212 Jan 06, 2023
Export transactions for an algorand wallet to a CSV file

algorand_txn_csv_exporter - (Algorand transaction CSV exporter) This script will export transactions for an algorand wallet to a CSV file. It is inten

TeneoPython01 5 Jun 19, 2022