msCentipede | hierarchical multiscale model for inferring transcription

by rajanil Python Version: v1.0 License: MIT

X-Ray Key Features Code Snippets(3)Community Discussions Vulnerabilities Install Support

kandi X-RAY | msCentipede Summary

msCentipede is a Python library. msCentipede has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

msCentipede is an algorithm for accurately inferring transcription factor binding sites using chromatin accessibility data (Dnase-seq, ATAC-seq) and is written in Python2.x and Cython. The hierarchical multiscale model underlying msCentipede identifies factor-bound genomic sites by using patterns in DNA cleavage resulting from the action of nucleases in open chromatin regions (regions typically bound by transcription factors). msCentipede, a generalization of the CENTIPEDE model, accounts for heterogeneity in the DNA cleavage patterns around sites bound by transcription factors. This code repository contains set of scripts to load the data and run the algorithm. The current document summarizes how to download and setup this software package and provides instructions on how to run the software on a test dataset of motif instances and some publicly available DNase-seq data.

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Quality

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Support

msCentipede has a low active ecosystem.

It has 23 star(s) with 6 fork(s). There are 5 watchers for this library.

It had no major release in the last 12 months.

There are 11 open issues and 10 have been closed. On average issues are closed in 24 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of msCentipede is v1.0

Quality

msCentipede has 0 bugs and 0 code smells.

Security

msCentipede has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

msCentipede code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

msCentipede is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

msCentipede releases are available to install and integrate.

Build file is available. You can build the component from source.

Installation instructions are not available. Examples and code snippets are available.

Top functions reviewed by kandi - BETA

kandi has reviewed msCentipede and discovered the below as its top functions. This is intended to give you an instant insight into msCentipede implemented functionality, and help decide if they suit your requirements.

Estimate optimal model .
Calculate read counts for given locations .
Parse command line arguments
Learn motifs .
Updates the likelihood function .
Infer the posterior posterior of the binding model .
Calculate square root function .
Compute the likelihood of a model .
Infer the footprint of the given model .
Plots a profile .

Get all kandi verified functions for this library.

msCentipede Key Features

No Key Features are available at this moment for msCentipede.

msCentipede Examples and Code Snippets

msCentipede,Executing the code

Python

Lines of Code : 46

License : Permissive (MIT)

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$ python call_binding.py

runs msCentipede, to infer transcription factor binding, given a set of motif
instances and chromatin accessibility data

positional arguments:
  motif_file            name of a gzipped text file containing positional

msCentipede,Executing the code,Plotting the factor-specific cleavage profile

Python

Lines of Code : 17

License : Permissive (MIT)

Copy

$ python plot_accessibility_profile.py

positional arguments
 motif_file            name of a gzipped text file containing positional
                        information and other attributes for motif instances
                        of a transcript

msCentipede,Getting the source code

Python

Lines of Code : 7

License : Permissive (MIT)

Copy

mkdir ~/proj
cd ~/proj
git clone https://github.com/rajanil/msCentipede

cd ~/proj/msCentipede
git fetch
git merge origin/master

python setup.py build_ext --inplace

Community Discussions

No Community Discussions are available at this moment for msCentipede.Refer to stack overflow page for discussions.

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install msCentipede

You can download it from GitHub.
You can use msCentipede 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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