Multiblock PLS
Multiblock PLS: Block dependent prediction modeling for Python - Published in JOSS (2019)
Python class defining a machine learning dataset ensuring key-based correspondence and maintaining integrity
Python class defining a machine learning dataset ensuring key-based correspondence and maintaining integrity - Published in JOSS (2017)
OpenOmics
OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases. - Published in JOSS (2021)
nplinker
A python framework for microbial natural products data mining by integrating genomics and metabolomics data
cosmosR
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
omicspls
R package for High dimensional data analysis and integration with O2PLS!
https://github.com/airbytehq/airbyte
The leading data integration platform for ETL / ELT data pipelines from APIs, databases & files to data warehouses, data lakes & data lakehouses. Both self-hosted and Cloud-hosted.
assignPOP
Population Assignment using Genetic, Non-genetic or Integrated Data in a Machine-learning Framework. Methods in Ecology and Evolution. 2018;9:439–446.
https://github.com/apache/airflow
Apache Airflow - A platform to programmatically author, schedule, and monitor workflows
harmonypy
🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
multimedia
multimedia is an R package for multimodal mediation analysis of microbiome data. It has been designed to help integration of relative abundance, survey, and metabolomic data through causal mediation analysis.
CMF
R package for finding a joint low-rank representation for a collection of matrices with shared row or column entities.
https://github.com/cthoyt/doctoral-thesis
📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology
https://github.com/cumbof/open-omics-api
A open-source framework for organising multi-omics data from heterogeneous data sources
https://github.com/fderuiter/imednet-python-sdk
A Unofficial Python SDK that makes it easy to work with the iMednet REST API from your code or the command line. Manage studies, subjects, records, and more with a "friendly" interface. No need to worry about the low-level details.
https://github.com/arenas-guerrero-julian/pg2rml-star
RML-star Mapping Bootstrapper from Property Graphs
https://github.com/bmascat/rna-seq-proteomics-pipeline
Multi-omics analysis of LFQ proteomics and transcriptomics of an ALMS1 gene knockout cell model after TGF-B pathway stimulation.
