pySCENIC | pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Ne | Genomics library
kandi X-RAY | pySCENIC Summary
kandi X-RAY | pySCENIC Summary
pySCENIC is a Python library typically used in Artificial Intelligence, Genomics applications. pySCENIC has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can install using 'pip install pySCENIC' or download it from GitHub, PyPI.
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
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Security
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Support
pySCENIC has a low active ecosystem.
It has 304 star(s) with 168 fork(s). There are 18 watchers for this library.
It had no major release in the last 12 months.
There are 117 open issues and 316 have been closed. On average issues are closed in 74 days. There are 3 open pull requests and 0 closed requests.
It has a neutral sentiment in the developer community.
The latest version of pySCENIC is 0.12.1
Quality
pySCENIC has 0 bugs and 0 code smells.
Security
pySCENIC has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
pySCENIC code analysis shows 0 unresolved vulnerabilities.
There are 0 security hotspots that need review.
License
pySCENIC is licensed under the GPL-3.0 License. This license is Strong Copyleft.
Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.
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pySCENIC releases are available to install and integrate.
Deployable package is available in PyPI.
Build file is available. You can build the component from source.
Top functions reviewed by kandi - BETA
kandi has reviewed pySCENIC and discovered the below as its top functions. This is intended to give you an instant insight into pySCENIC implemented functionality, and help decide if they suit your requirements.
- Return a dict of cmdclass for the given cmdclass
- Create a ConfigParser instance from a root
- Read file contents
- Get the project root directory
- Extract version information from VCS
- Create an argument parser
- Add motif annotation parameters
- Argument specific to the loom file
- Add the computation parameters
- Run the main function
- Construct a FeatureSeq from a BED file
- Derives the threshold for a given strategy
- Convert modules to Regulons
- Deploy pyscenic
- Calculate the rho of x and y
- Scans the setup py file and checks if it is missing
- Convert a module to a Regulon
- Read the content of a file
- Run motifs
- Add correlation coefficient
- Find motifs in RNF
- Calculate cellular enrichment
- Extract version information from setup py
- Create the versioneer config file
- Export to loom format
- Prune targets
- Find the adjacency matrix
Get all kandi verified functions for this library.
pySCENIC Key Features
No Key Features are available at this moment for pySCENIC.
pySCENIC Examples and Code Snippets
How to make Python package update within a code to take effect on-the-fly
Python
Lines of Code : 6License : Strong Copyleft (CC BY-SA 4.0)
Lines of Code : 6License : Strong Copyleft (CC BY-SA 4.0)
Copy#!/usr/bin/env bash
pip install pyscenic==0.10.0
python first_script.py
pip install pyscenic==0.10.4
python second_script.py
How to make Python package update within a code to take effect on-the-fly
PythonLines of Code : 70License : Strong Copyleft (CC BY-SA 4.0)
Lines of Code : 70License : Strong Copyleft (CC BY-SA 4.0)Copy# Copyright © 2021 Alexander L. Hayes
# MIT License
git clone git@github.com:aertslab/pySCENIC pySCENIC100
git clone git@github.com:aertslab/pySCENIC pySCENIC104
(
cd pySCENIC100
git checkout 0.10.0
sed -i "s/pyscenic/pyscenic100/gCommunity Discussions
Trending Discussions on pySCENIC
QUESTION
How to make Python package update within a code to take effect on-the-fly
Asked 2021-Apr-29 at 19:44
I have the following line of codes:
...ANSWER
Answered 2021-Apr-21 at 13:28If you are able to, a simple solution would be to write a bash file running sequentially two python files, with a change of version of the package pyscenic between the two python runs using pip. You can do something similar to this, like:
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install pySCENIC
You can install using 'pip install pySCENIC' or download it from GitHub, PyPI.
You can use pySCENIC like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
You can use pySCENIC like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
Support
For any new features, suggestions and bugs create an issue on GitHub.
If you have any questions check and ask questions on community page Stack Overflow .
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