1. Prerequisites

These programs must be installed and callable from the command line:

• Python 3

• Samtools

• bowtie2 (Only needed if your input is fastq file)

2. Python Dependencies

• MACS2

• pysam

• pyBigWig

• numpy

• scipy

Note

These packages will be installed automatically if you use pip3.

3. Install Spiker

Use pip3 to install spiker from PyPI or github.

$ pip3 install spiker
or
$ pip3 install git+https://github.com/liguowang/spiker.git

4. Upgrade Spiker

$ pip3 install spiker --upgrade

5. Uninstall

$ pip3 uninstall spiker