peako | PeaKO discovers motifs in ChIP-seq datasets

by hoffmangroup Python Version: 0.0.6 License: Non-SPDX

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

kandi X-RAY | peako Summary

peako is a Python library. peako has no bugs, it has no vulnerabilities, it has build file available and it has low support. However peako has a Non-SPDX License. You can install using 'pip install peako' or download it from GitHub, PyPI.

PeaKO discovers motifs in ChIP-seq datasets with knockout controls. PeaKO takes in paired wild-type/knockout BAM files in addition to several reference files, as input. It returns a file of ranked motifs (see our paper for more details).

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Quality

Security

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Support

peako has a low active ecosystem.

It has 2 star(s) with 0 fork(s). There are 2 watchers for this library.

It had no major release in the last 12 months.

There are 0 open issues and 1 have been closed. On average issues are closed in 4 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of peako is 0.0.6

Quality

peako has no bugs reported.

Security

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

License

peako has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

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

Deployable package is available in PyPI.

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

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

Top functions reviewed by kandi - BETA

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

Main entry point .
Writes a dictionary of motifs to a csv file .
Load data from html file .
Reads the centrimo_exacto_predictiono_df from a file .
Read and sort the centrimo data from a file .
Remove motifs from a CentriMoDataframe .
Parse html file .
Read CentriMo data from a file .
Append a suffix to the motif id .
Check if file exists .

Get all kandi verified functions for this library.

peako Key Features

No Key Features are available at this moment for peako.

peako Examples and Code Snippets

No Code Snippets are available at this moment for peako.

Community Discussions

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

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

Vulnerabilities

No vulnerabilities reported

Install peako

NOTES: If you run into errors indicating missing bs4 or pyYAML packages, try running pip3 install beautifulsoup4==4.8.2 pyyaml. If step 2 above fails to create a Conda environment, you may try: conda create --name peako conda activate peako # or source activate peako conda install python=3.7 conda install -c anaconda beautifulsoup4=4.7 pandas conda install -c bioconda -c conda-forge -c anaconda snakemake-minimal flake8 pathlib2 ipython twine conda install -c bioconda pybedtools Please note that we have only tested peaKO on Linux.
Download peaKO's environment file.
Open a terminal and run conda env create -f peako-env.yml in your Downloads directory. This will create a Conda environment called "peako".
Run conda activate peako or source activate peako to activate this environment.
Install peaKO from PyPI by running python3 -m pip install peako.
You can test that this worked by running peako --help.

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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