HandyEnrich Installation and User Manual

Overview of HandyEnrich

HandyEnrich is a software package for enrichment analysis which enables multiple enrichment tests with a simple command

Supported Environment

1. HandyEnrich can be executed on Linux OS / Mac

Software Dependency

Required

1. Python3 (version: 3.7.0 or later) with statsmodels/scipy module required

Software installation

Each installation step will take less than ~1 min

Installation of HandyEnrich

1. Download HandyEnrich by

    git clone https://github.com/UTNK/handyenrich.git

2. Add the absolute path of handyenrich/src directory to $PATH

3. Make handyenrich/src/* executable

   chmod u+x handyenrich/src/*

Sample Codes

The HandyEnrich package contains an example input file in the examples directory so users can check the software functions as follows:

Example 1

Test enrichment of metagenome samples in environment ontology terms

entest -r metagenome/meo_mg.txt -q metagenome/query.txt 

Input:

meo_mg.txt

query.txt

Output:

Standard output: stats, p values, q values for each environment ontology term ("meo")

Usage

usage: entest [-h] [-v] [-r REF] [-q QUERY] [-a ALL] [-d DELIM1]
              [--delim2 DELIM2] [--alt ALT] [--cor COR]

entest

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         Print version
  -r REF, --ref REF     File path of Class-Term list
  -q QUERY, --query QUERY
                        File path of query term list
  -a ALL, --all ALL     File path of all term list
  -d DELIM1, --delim1 DELIM1
                        delimitter between class and term
  --delim2 DELIM2       delimitter among terms
  --alt ALT             Alternative hypothesis type ("greater" :default,
                        "less", "two-sided")
  --cor COR             Multiple test correction default: fdr_bh (see https://
                        www.statsmodels.org/dev/generated/statsmodels.stats.mu
                        ltitest.multipletests.html)

Contact

Naoki Konno (The University of Tokyo) naoki@bs.s.u-tokyo.ac.jp