Correlation Trait Loci (CTL) mapping
Correlation Trait Loci (CTL) mapping: phenotype network inference subject to genotype - Published in JOSS (2016)
omicspls
R package for High dimensional data analysis and integration with O2PLS!
https://github.com/cwieder/py-sspa
Single sample pathway analysis tools for omics data
deconvR
The deconvR is an R package designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model.
aggmap
Jigsaw-like AggMap: A Robust and Explainable Multi-Channel Omics Deep Learning Tool
https://github.com/cran-task-views/omics
CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics
volcano3d
An R package to plot interactive three-way differential expression analysis
https://github.com/a-r-j/tb-resources
List of online databases and resources for Mycobacterium Tuberculosis
deco
DECO :: Decomposing heterogeneous population cohorts for patient stratification and discovery of biomarkers using omic data profiling. R package
https://github.com/berenslab/sbnn
A sparse bottleneck neural network to predict electrophysiological properties of neurons from their gene expression.
https://github.com/computationalproteomics/omicloupe
Understanding expression across comparisons and datasets through interactive visualization
https://github.com/fgcz/bfabricshiny
Manage life sciences data using R and b-fabric - a WSDL/REST interface and a tool box; main focus on MS data
https://github.com/biomedsciai/geno4sd
An python omics data toolkit for the analysis across biological scales
https://github.com/cumbof/open-omics-api
A open-source framework for organising multi-omics data from heterogeneous data sources
https://github.com/broadinstitute/celligner2
A new version of the celligner package using VAEs. Inspired from the Theis lab's scArches.
https://github.com/cafferychen777/microbiomestat-turtorial-professional-version
MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.
splineomics
Timeseries analysis of -omics data can be carried out by fitting spline curves to the data and using limma for hypothesis testing. The obtained hits can be clustered based on the spline shape and then used for an overrepresentation (ORA) analysis.The R package SplineOmics streamlines this whole process and generates reports
masssight
An R package for the alignment and scaling of LC-MS metabolomics data
https://github.com/cafferychen777/microbiomestat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
holofood-database
HoloFood is a project investigating sustainable food production through hologenomics. This Django app is the data portal where samples and other datasets from the project are made publicly available.
translational-omics-ad
This is the lesson repository for the Workshop on Computational Techniques and Resources for Effective Translational Research in Alzheimer's Disease.