SICERpy | Python wrapper around the popular ChIP-Seq peak caller SICER

by dariober Python Version: Current License: No License

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

kandi X-RAY | SICERpy Summary

SICERpy is a Python library. SICERpy has no bugs, it has no vulnerabilities and it has low support. However SICERpy build file is not available. You can download it from GitHub.

SICER is a popular peak caller particularly suitable for detection of broad ChIP-Seq marks. However, I found the original master script, SICER.sh, clunky to use.

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Support

SICERpy has a low active ecosystem.

It has 13 star(s) with 4 fork(s). There are 3 watchers for this library.

It had no major release in the last 6 months.

There are 0 open issues and 10 have been closed. On average issues are closed in 83 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of SICERpy is current.

Quality

SICERpy has no bugs reported.

Security

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

License

SICERpy does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

SICERpy releases are not available. You will need to build from source code and install.

SICERpy has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

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

Combine read copy_copy_distribution
Given a list of bed_list return a list of BEDs that match the strand
Combine two histograms
Return a list of keys
Find the index of the value in a poisson distribution
Poisson poisson function
Compute the fact
Logarithm of a logarithm
Filter reads that are added to the end of a BED file
Write an item to a file
Find regions above a given threshold
Find islands above the given threshold
Count the number of lines in a file
Normalize tag count
Combine overlapping islands
Filter reads based on cutoff
Writes a chromosome to a file
Get the number of bed values
Write a list of Bed6_List to a file
Returns a list of islands with the given threshold
List of keys

Get all kandi verified functions for this library.

SICERpy Key Features

No Key Features are available at this moment for SICERpy.

SICERpy Examples and Code Snippets

No Code Snippets are available at this moment for SICERpy.

Community Discussions

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

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

Vulnerabilities

No vulnerabilities reported

Install SICERpy

SICER.py requires python 2.6+ with scipy package as per the original version. In addition it requires the pysam package.
Best: Create a symlink from SICER.py to a directory somewhere on your PATH and execute SICER.py [options], e.g.
Call using full path /path/to/SICERpy/SICER.py [options]
Add the whole directory SICERpy to your PATH variable.

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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