profiling-workflow-demo

https://github.com/niranjchandrasekaran/profiling-workflow-demo

Science Score: 44.0%

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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Scientific vocabulary similarity
Low similarity (9.7%) to scientific vocabulary

Last synced: 11 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: niranjchandrasekaran
License: bsd-3-clause
Language: Jupyter Notebook
Default Branch: master
Size: 9.63 MB

Statistics

Stars: 0
Watchers: 1
Forks: 1
Open Issues: 0
Releases: 0

Created almost 4 years ago · Last pushed almost 3 years ago

Metadata Files

Readme License Audit Citation

This repository was created from the cytomining/profiling-template template repository. The README.md of that repository and that of cytomining/profiling-recipe contain instructions on how to - create a data repository - weld profiling-recipe to the data repository - create the folder structure and populating them with the necessary files - edit the config.yml file - run the profiling recipe

To reproduce the profiles in this repo, clone the repo (with git's git-lts extension)

bash git clone git@github.com:niranjchandrasekaran/profiling-workflow-demo.git

Installation

External dependencies

To plot the results first install orca.

Python dependencies

You can then use conda (traditional way) or poetry (new way) to install the dependencies:

Conda

Install miniconda (we use Anaconda as our package manager. Install Miniconda following the instructions here) and git-lfs

Install the conda environment

cd profiling-workflow-demo conda env create --force --file environment.yml conda activate profiling

and then run the following command

bash python profiling-recipe/profiles/profiling_pipeline.py --config config_files/config.yml

Poetry

Set up poetry. It will automatically create a new virtual environment for this project with python 3.8.

cd profiling-workflow-demo poetry install

Then, to produce the figures and statistics again you can do cd analysis poetry run jupyter notebook 0.calculate-ap.py

Owner

Name: Niranj Chandrasekaran
Login: niranjchandrasekaran
Kind: user
Company: @broadinstitute

Website: niranjchandrasekaran.com
Repositories: 2
Profile: https://github.com/niranjchandrasekaran

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this template, please cite it as below."
authors:
- family-names: "Chandrasekaran"
  given-names: "Srinivas Niranj"
  orcid:  "https://orcid.org/0000-0001-8874-9988"
- family-names: "Way"
  given-names: "Gregory"
  orcid: "https://orcid.org/0000-0002-0503-9348"
- family-names: "Carpenter"
  given-names: "Anne"
  orcid: "https://orcid.org/0000-0003-1555-8261"
- family-names: "Singh"
  given-names: "Shantanu"
  orcid: "https://orcid.org/0000-0003-3150-3025"
title: "Broad Institute Imaging Platform Profiling Template"
url: "https://github.com/cytomining/profiling-template"

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