https://github.com/bigbio/sdrf-pipelines
`sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files
proteomics-sample-metadata
The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
TDbasedUFE
This is a R package that intends to perform all the features possible by tensor decomposition based unsupervised feature extraction
https://github.com/alok-ai-lab/deepinsight3d_pkg
DeepInsight3D package to deal with multi-omics or multi-layered data
movis
MOVIS: A Multi-Omics Software Solution for Multi-modal Time-Series Clustering, Embedding, and Visualizing Tasks, by Aleksandar Anžel, Dominik Heider, and Georges Hattab
ramen
Regional Association of Methylation variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify Variable Methylated Regions (VMRs) in microarray DNA methylation data. Additionally, using Genotype (G) and Environmental (E) data, it can identify which G, E, G+E or GxE model better explains this variability.
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.