Test reproducibility of leiden/umap on different systems

Last update: Oct 16, 2021

Related tags

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/

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

3 Oct 24, 2022

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

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

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. Can be runned via dmenu or rofi.

2 Jan 12, 2022

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

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

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

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

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

91 Dec 28, 2022

Comments

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)

containers-0.1.0(Oct 16, 2021)

Release to hold singularity container as assets.
Source code(tar.gz)
Source code(zip)
scanpy_reproducibility.sif(424.00 MB)

Owner

Gregor Sturm

Always stay curious!

GitHub Repository https://grst.github.io/scanpy_reproducibility/

An event-based script that is designed to improve your aim

Aim-Trainer Info: This is an event-based script that is designed to improve a user's aim. It was built using Python Turtle and the Random library. Ins

4 Feb 17, 2022

Empresas do Brasil (CNPJs)

Biblioteca em Python que coleta informações cadastrais de empresas do Brasil (CNPJ) obtidas de fontes oficiais (Receita Federal) e exporta para um formato legível por humanos (CSV ou JSON).

8 Aug 17, 2022

An easy python calculator for those who want's to know how if statements, loops, and imports works give it a try!

A usefull calculator for any student or anyone who want's to know how to build a simple 2 mode python based calculator.

1 Jan 06, 2022

This repository contains the exercices for the robotics class at Supaero, 2022.

Supaero robotics, 2022 This repository contains the exercices for the robotics class at Supaero, 2022. The exercices are organized by notebook. Each n

5 Aug 01, 2022

Pengenalan para anggota KOMPETEGRAM

Pengenalan Anggota KOMPETEGRAM Apa isi repositori ini ? 💬 Repositori ini berisi pengenalan nama anggota KOMPETEGRAM dari seluruh angkatan atau Batch.

7 Sep 17, 2022

A git extension for seeing your Cloud Build deployment

13 May 10, 2022

Svg-turtle - Use the Python turtle to write SVG files

SaVaGe Turtle Use the Python turtle to write SVG files If you're using the Pytho

7 Dec 21, 2022

This repository collects nice scripts ("plugins") for the SimpleBot bot for DeltaChat.

Having fun with DeltaChat This repository collects nice scripts ("plugins") for the SimpleBot bot for DeltaChat. DeltaChat is a nice e-mail based mess

3 Dec 25, 2021

Blender addon, import and update mixamo animation

This is a blender addon for import and update mixamo animations.

7 Apr 19, 2022

Use this function to get list of routes for particular journey

route-planner Functions api_processing Use this function to get list of routes for particular journey. Function has three parameters: Origin Destinati

2 Nov 28, 2021

Customer Service Requests Analysis is one of the practical life problems that an analyst may face. This Project is one such take. The project is a beginner to intermediate level project. This repository has a Source Code, README file, Dataset, Image and License file.

Customer Service Requests Analysis Project 1 DESCRIPTION Background of Problem Statement : NYC 311's mission is to provide the public with quick and e

7 Sep 19, 2022

An attempt at furthering Factorio Calculator to work in more general contexts.

factorio-optimizer Lets do Factorio Calculator but make it optimize. Why not use Factorio Calculator? Becuase factorio calculator is not general. The

1 Jun 03, 2022

Visual Python and C++ nanosecond profiler, logger, tests enabler

Look into Palanteer and get an omniscient view of your program Palanteer is a set of lean and efficient tools to improve the quality of software, for

1.9k Dec 26, 2022

APRS Track Direct is a collection of tools that can be used to run an APRS website

APRS Track Direct APRS Track Direct is a collection of tools that can be used to run an APRS website. You can use data from APRS-IS, CWOP-IS, OGN, HUB

42 Dec 29, 2022

A PowSyBl and Python integration based on GraalVM native image

PyPowSyBl The PyPowSyBl project gives access PowSyBl Java framework to Python developers. This Python integration relies on GraalVM to compile Java co

23 Dec 14, 2022

Scripts to convert the Ted-MDB corpora into the formats for DISRPT shared task and the converted corpora

Scripts to convert the Ted-MDB corpora into the formats for DISRPT shared task and the converted corpora.

1 Feb 08, 2022

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

108 Jan 08, 2023

Test reproducibility of leiden/umap on different systems

Related tags

Overview

Test reproducibility of leiden/umap on different systems

Running the pipeline

Results

You might also like...

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

Leveraging pythonic forces to defeat different coding challenges 🐍

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

Moji sends text and fun facts from different APIs wit da use of a notification deamon

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

Different steganography methods with examples and my own small image database

Structural basis for solubility in protein expression 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.

ASVspoof 2021 Baseline Systems

Comments

Inquiry: any explanations?

Releases(containers-0.1.0)

containers-0.1.0(Oct 16, 2021)

Owner

Gregor Sturm

An event-based script that is designed to improve your aim

Empresas do Brasil (CNPJs)

An easy python calculator for those who want's to know how if statements, loops, and imports works give it a try!

This repository contains the exercices for the robotics class at Supaero, 2022.

Pengenalan para anggota KOMPETEGRAM

A git extension for seeing your Cloud Build deployment

Svg-turtle - Use the Python turtle to write SVG files

This repository collects nice scripts ("plugins") for the SimpleBot bot for DeltaChat.

Blender addon, import and update mixamo animation

Use this function to get list of routes for particular journey

Customer Service Requests Analysis is one of the practical life problems that an analyst may face. This Project is one such take. The project is a beginner to intermediate level project. This repository has a Source Code, README file, Dataset, Image and License file.

An attempt at furthering Factorio Calculator to work in more general contexts.

Visual Python and C++ nanosecond profiler, logger, tests enabler

APRS Track Direct is a collection of tools that can be used to run an APRS website

A PowSyBl and Python integration based on GraalVM native image

Scripts to convert the Ted-MDB corpora into the formats for DISRPT shared task and the converted corpora

Hydralit package is a wrapping and template project to combine multiple independant Streamlit applications into a multi-page application.

Table (Finnish Taulukko) glued together to transform into hands-free living.

This is a small compiler to demonstrate how compilers work.

Small Arrow Vortex clipboard processing library