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/
Script to calculate delegator epoch returns for all pillars

znn_delegator_calculator Script to calculate estimated delegator epoch returns for all Pillars, so you can delegate to the best one. You can find me o

2 Dec 03, 2021
Generates Windows 95 and 95 OEM keys using the modulus 7 check algorithm

w95keygen-python windowskeygen.py - Generates Windows 95 and 95 OEM keys using the modulus 7 check algorithm Just download and drop in the directory y

Joshua Alto 1 Dec 06, 2021
Repository for DNN training, theory to practice, part of the Large Scale Machine Learning class at Mines Paritech

DNN Training, from theory to practice This repository is complementary to the deep learning training lesson given to les Mines ParisTech on the 11th o

Alexandre Défossez 6 Nov 14, 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
Return-Parity-MDP - Towards Return Parity in Markov Decision Processes

Towards Return Parity in Markov Decision Processes Code for the AISTATS 2022 pap

Jianfeng Chi 3 Nov 27, 2022
An app about keyboards, originating from the design of u/Sonnenschirm

keebapp-backend An app about keyboards, originating from the design of u/Sonnenschirm Setup Firstly, ensure that the environment for python is install

8 Sep 04, 2022
This library is an abstraction for Splunk-related development, maintenance, or migration operations

This library is an abstraction for Splunk-related development, maintenance, or migration operations. It provides a single CLI or SDK to conveniently perform various operations such as managing a loca

NEXTPART 6 Dec 21, 2022
Hashcrack - A non-object oriented open source, Software for Windows/Linux made in Python 3

Multi Force This project is a non-object oriented open source, Software for Wind

Radiationbolt 3 Jan 02, 2023
[arXiv 2020] Video Representation Learning with Visual Tempo Consistency

Video Representation Learning with Visual Tempo Consistency [Paper] [Project Page] News Full codebae is coming soon Pretained Models For now, we provi

DeciForce: Crossroads of Machine Perception and Autonomy 24 Nov 23, 2022
This is a python package to get wards, districts,cities and provinces in Zimbabwe

Zim-Places Features This is a python package that allows you to search for cities, provinces, and districts in Zimbabwe.Zimbabwe is split into eight p

RONALD KANYEPI 2 Mar 01, 2022
Pattern Matching for Python 3.7+ in a simple, yet powerful, extensible manner.

Awesome Pattern Matching (apm) for Python pip install awesome-pattern-matching Simple Powerful Extensible Composable Functional Python 3.7+, PyPy3.7+

Julian Fleischer 97 Nov 03, 2022
Monochrome's API, implemented with Deta Base and Deta Drive.

Monochrome Monochrome's API, implemented with Deta Base and Deta Drive. Create a free account on Deta to test this out! Most users will prefer the Mon

Monochrome 5 Sep 22, 2022
Markov Chain Composer

Markov Chain Composer Using Markov Chain to represent relationships between words in song lyrics and then generating new lyrics.. ahem interpretive po

Kylie 85 Dec 09, 2022
Regular Expressions - Use regular expressions to detect date format

A list of all the resources used https://regex101.com/ - To test regex https://w

Ravika Nagpal 1 Jan 04, 2022
sumCulator Это калькулятор, который умеет складывать 2 числа.

sumCulator Это калькулятор, который умеет складывать 2 числа. Но есть условия: Эти 2 числа не могут быть отрицательными (всё-таки это вычитание, а не

0 Jul 12, 2022
Enjoyable scripting experience with Python

Enjoyable scripting experience with Python

8 Jun 08, 2022
Fork of pathlib aiming to support the full stdlib Python API.

pathlib2 Fork of pathlib aiming to support the full stdlib Python API. The old pathlib module on bitbucket is in bugfix-only mode. The goal of pathlib

Jazzband 73 Dec 23, 2022
List of resources for learning Category Theory

A curated list of resources for studying category theory. As resources aimed at mathematicians are abundant, this list is aimed at materials whose target audience is not people with a graduate-level

Bruno Gavranović 100 Jan 01, 2023
Hydralit package is a wrapping and template project to combine multiple independant Streamlit applications into a multi-page application.

Hydralit The Hydralit package is a wrapping and template project to combine multiple independant (or somewhat dependant) Streamlit applications into a

Jackson Storm 108 Jan 08, 2023
A tool to quickly create codeforces contest directories with templates.

Codeforces Template Tool I created this tool to help me quickly set up codeforces contests/singular problems with templates. Tested for windows, shoul

1 Jun 02, 2022