exprmat

exprmat (short for expression matrix) is a routine package for manipulation of sparse expression matrices. It provides a structured, introspective mudular interface for man and machine.

You may refer to these places:

• Source code repository
• Releases in PyPI
• Documentation

Database installation

The package exprmat do not come with its reference database. You need to setup the database and configure the package to find it properly, or else most of the features from the package will fail.

This package ships with a tool to fetch database distribution on Alibaba Cloud object storage service. You will first need to register an account and request a key-secret pair to authenticate your identity, before starting out to download specified version of the database distribution using the tool bsync-fetch installed alongside the exprmat package.

usage: bsync-fetch [-h] --id ID --secret SECRET 
                        --bucket BUCKET [--endpoint ENDPOINT] --version VERSION

fetch from remote bucket.

options:
  -h, --help           show this help message and exit
  --id ID              The requester access id.
  --secret SECRET      The requester access secret.
  --bucket BUCKET      The name of the bucket.
  --endpoint ENDPOINT  The domain names that other services can use to access OSS.
  --version VERSION    The version to fetch from remote.

Suppose you are installing the database version 0.1.50 to ~/database.

# enter the intended path of installation
cd ~/database

# download the version 0.1.50 of database distribution
# you must download the same version of the database with the package. the database
# and package content are published strictly synchronically.
bsync-fetch --id <your-id> --secret <your-api-secret> \
            --bucket exprmat-data --endpoint oss-cn-wuhan-lr.aliyuncs.com \
            --version 0.1.50

The authentication tokens passed to --id and --secret is provided by the Alibaba Cloud service (See the Documentation for details)

Licensing

The original part of the source code is licensed under GNU GPLv3. The database download tool bsync-fetch (developed as a dependency package for exprmat, in python package bincsync) is only allowed for internal use and not for re-distribution.

exprmat - Routines to manipulate expression matrices
Copyright (C) 2025 - 2026 Zheng Yang <xornent@outlook.com>

exprmat is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions. 
You should have received a copy of the GNU General Public License
version 3 along with this program. If not, see <http://www.gnu.org/licenses/>.

The GNU General Public License does not permit incorporating 
your program into proprietary programs.

I acknowledge the following author(s) for modifying and integrating their work in the form of source code to this package.

• scanpy, BSD 3-Clause, Copyright (c) 2017 F. Alexander Wolf, P. Angerer, Theis Lab
• snapatac2, MIT, Copyright (c) 2022-2024 Kai Zhang
• sc3s, GNU GPLv3, Copyright (c) Quah, F.X. and Hemberg, M. and contributors.
• cnmf, MIT, Copyright (c) 2019 Dylan Kotliar
• infercnvpy, BSD 3-Clause, Copyright (c) 2022, Gregor Sturm
• tape, GNU GPLv3, Copyright (c) The contributors.
• metaq, MIT, Copyright (c) 2024 XLearning Group
• scenicplus, Academic Non-commercial Software License Agreement, Copyright (c) The contributors.
• lianapy, BSD 3-Clause, Copyright (c) 2025, Daniel Dimitrov
• idr, GNU GPLv2, Copyright (c) The contributors
• omicverse, GNU GPLv3, Copyright (c) 2024 112 Lab
• pydiffmap, MIT, Copyright (c) 2018 Ralf Banisch, Erik Henning Thiede, Zofia Trstanova
• scfates, BSD 3-Clause, Copyright (c) 2020, Louis Faure
• cytotrace2, Stanford Non-commercial Software License Agreement, Copyright (c) The contributors.
• scvelo, BSD 3-Clause, Copyright (c) 2018, Theis Lab
• pydeseq2, MIT, Copyright (c) 2022 Owkin
• decoupler, GNU GPLv3, Copyright (c) The contributors.
• scvitools, BSD 3-Clause, Copyright (c) 2026, Yosef Lab, Weizmann Institute of Science
• spacec, Academic Software License Agreement, Copyright (c) The contributors.
• squidpy, BSD 3-Clause, Copyright (c) 2021, Theis Lab
• sctransformpy, GNU GPLv3, Copyright (c) David DeTomaso
• magic, GNU GPLv2, Copyright (c) The contributors.
• scrublet, MIT, Copyright (c) 2018 Samuel Wolock
• py8rds, MIT, Copyright (c) 2024 Cellular Genetics Informatics
• nimfa, New BSD, Copyright (c) 2016 The Nimfa developers.
• cellnest, GNU GPLv3, Copyright (c) The contributors.
• tangram, BSD 3-Clause, Copyright (c) 2020, Broad Institute All rights reserved.
• deepst, MIT, Copyright (c) 2022 spatial-Transcriptomics
• spagcn, MIT, Copyright (c) 2020 JianHu
• spatialde, MIT, Copyright (c) 2018 Teichmann Group
• omnipathdb, See source licenses and permissions.