PyPI

It is recommended to install lisa to a virtual environment:

$ python3 -m venv .venvs/lisa_env
$ source .venvs/lisa_env/bin/activate

Install LISA to this virtual env using this command:

(lisa_env) $ pip install lisa2

Conda

First, create a virtual environment:

(base) $ conda create --name lisa_env
(base) $ conda activate lisa_env

Then install from Conda:

(lisa_env) $ conda install -c liulab-dfci lisa2

Dataset Installation Issues

If you successfully install lisa but the program fails while downloading data, follow these manual dataset installation instructions.

Command Line Interface

LISA’s cli offers convenient methods for the most common use cases. See the API, or try:

(lisa_env) $ lisa {command} --help

for parameter descriptions. See the User Guide for best practices.

Python Interface

The python module allows more control over the LISA test and more convenient data analysis. See the Python API and the User Guide.

Removed

Removed coverage test from base LISA install because pyBigWig was causing problems with installation. Now, to install the coverage test, do

$ pip install lisa2[coverage]

Changed

• Loosening H5py requirements for easier install.

[2.2.4] - 2021-03-01

• Added “lisa deseq” interface for parsing DESeq2 output files for fast LISA tests of DE genes

[2.2.0] - 2021-01-10

Added

• Added “FromRegions” test, and moved all older functionalities to “FromGenes”. New feature allows user to run LISA test with their own regions-of-interest

• Added “query_reg_score” and “background_reg_score” matrices to output metadata of “FromRegions” test, which allows user to see which genes are likely regulated by each factor.

• New backend interface for faster file transfers

• Added ability to append more data to backend for future updates, including ATAC-seq epigenetic backgrounds

• Added more documentation and user guide

• Appended new ATAC data and reprocessed motifs using JASPAR database

Removed

• Removed “cores” option from multi and oneshot tests, and removed mutliprocessing from package.

• Removed “one-vs-rest” test because proved to provide unstable results

[2.1.0] - 2020-12-01

• Bugfixes in output of “lisa multi” test

• Refactored classes for future extension to user-supplied fragment files and peaks

• Added integration testing

• Added factor accessibility introspection to results printout

• Made RP maps substitutable for future tests

• Made assays modular so users can specify which statistical tests they are interested in

[2.0.6] - 2020-11-22

• Support for Lisa version 1 API for integration with LISA website

• Bugfixes in motif mode results

• Slight speedups in parallelization of insilico-delition computing