Metadata-Version: 2.1
Name: chipseqpeaks
Version: 1.1.1
Summary: Easy management of ChIP-seq peak calling
Home-page: https://github.com/anthony-aylward/chipseqpeaks.git
Author: Anthony Aylward, Joshua Chiou
Author-email: aaylward@eng.ucsd.edu
License: UNKNOWN
Description: # chipseqpeaks
        
        A wrapper for MACS2 that abstracts out some things and makes it easier to use.
        Thanks due to Joshua Chiou for inspiration and contributions.
        
        > **Warning:** Before using chipseqpeaks, please make sure that one of the
        > environment variables TMPDIR, TEMP, or TMP is set to an appropriate path.
        > This is the only way to ensure MACS2 writes temporary files to the correct
        > location, and failing to do so may cause errors on some systems. (ง •̀_•́)ง
        
        ## Installation
        
        ```sh
        pip3 install chipseqpeaks
        ```
        
        or
        
        ```sh
        pip3 install --user chipseqpeaks
        ```
        
        ## Example API usage
        ```python
        from chipseqpeaks import ChIPSeqPeaks
        with ChIPSeqPeaks(<bytes object or path to BAM file>) as cp:
            cp.cleans_up = False
            cp.remove_blacklisted_peaks(<path/to/blacklist.bed>)
            cp.write(<output prefix>)
        ```
        
        ## Example command line usage
        
        For help text, see:
        ```sh
        chipseqpeaks-call -h
        ```
        For ChIP-seq:
        ```sh
        chipseqpeaks-call --control input.bam chip.bam
        ```
        
        For ATAC-seq:
        ```sh
        chipseqpeaks-call --atac-seq atac.bam
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
