Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
awesome-rm-omics
List of software packages for repeated measures analysis in -omics data
https://github.com/smdabdoub/awesome-rm-omics
Last synced: 3 days ago
JSON representation
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Software packages and methods
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Spline Modeling
- A Linear Mixed Model Spline Framework for Analysing Time Course ‘Omics’ Data
- **SplinectomeR** - Shields-Cutler - [SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies](https://doi.org/10.3389/fmicb.2018.00785)
- **MetaLonDA** - Metwally - [MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies](https://doi.org/10.1186/s40168-018-0402-y) - [vignette](https://cran.r-project.org/web/packages/MetaLonDA/vignettes/MetaLonDA.html)
- A Linear Mixed Model Spline Framework for Analysing Time Course ‘Omics’ Data
- **metaDprof** - Luo - [An informative approach on differential abundance analysis for time-course metagenomic sequencing data](https://doi.org/10.1093/bioinformatics/btw828)
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Linear/Mixed Modeling
- **ZIBR** - Chen - zero-inflated Beta regression - [A two-part mixed-effects model for analyzing longitudinal microbiome compositional data](https://doi.org/10.1093/bioinformatics/btw308)
- **LassoGLMMforMicrobiomes** - Tipton - lasso-penalized generalized linear mixed model (LassoGLMM) with variable selection - [Measuring associations between the microbiota and repeated measures of continuous clinical variables using a lasso-penalized generalized linear mixed model](https://doi.org/10.1186/s13040-018-0173-9)
- **MALLARD** - Silverman - [Dynamic linear models guide design and analysis of microbiota studies within artificial human guts](https://doi.org/10.1186/s40168-018-0584-3)
- **BEEM** - Li - [An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data](https://doi.org/10.1186/s40168-019-0729-z)
- **NBZIMM** - Zhang - [NBZIMM: negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis](https://doi.org/10.1186/s12859-020-03803-z) - [vignette](https://abbyyan3.github.io/NBZIMM-tutorial/)
- **MiRKAT-MC** - Jiang - [MiRKAT-MC: A Distance-Based Microbiome Kernel Association Test With Multi-Categorical Outcomes](https://doi.org/10.3389/fgene.2022.841764) - [vignette](https://cran.r-project.org/web/packages/MiRKAT/vignettes/MiRKAT_Vignette.html)
- **coda4microbiome** - Calle - [coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies](https://doi.org/10.1186/s12859-023-05205-3)
- **ZIBR** - Chen - zero-inflated Beta regression - [A two-part mixed-effects model for analyzing longitudinal microbiome compositional data](https://doi.org/10.1093/bioinformatics/btw308)
- Fast zero-inflated negative binomial mixed modeling approach for analyzing longitudinal metagenomics data
- Fast zero-inflated negative binomial mixed modeling approach for analyzing longitudinal metagenomics data
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Stochastic/Probabilistic Modeling
- **TGP-CODA** - Äijö - [Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing](https://doi.org/10.1093/bioinformatics/btx549)
- **LUMINATE** - Joseph - [Efficient and Accurate Inference of Mixed Microbial Population Trajectories from Longitudinal Count Data](https://doi.org/10.1016/j.cels.2020.05.006)
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Machine Learning/Artificial Neural Networks (Deep Learning) Methods
- **DIVERS** - Ji - [Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling](https://doi.org/10.1038/s41592-019-0467-y)
- **phyLoSTM** - Sharma - combined modeling using CNN for feature extraction and LSTM for temporal dependency analysis - [phyLoSTM: a novel deep learning model on disease prediction from longitudinal microbiome data](https://doi.org/10.1093/bioinformatics/btab482)
- **EMBED** - Shahin - [EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies](https://doi.org/10.1038/s41540-023-00285-6)
- **TEMPTED** - Shi - [Time-Informed Dimensionality Reduction for Longitudinal Microbiome Studies](https://doi.org/10.1101/2023.07.26.550749)
- A review on longitudinal data analysis with random forest
- A review on longitudinal data analysis with random forest
- A review on longitudinal data analysis with random forest
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Ecology Literature
- **pldist** - Plantinga - [pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis](https://doi.org/10.1093/bioinformatics/btz120)
- Multivariate methods for testing hypotheses of temporal community dynamics - [paper 2](https://doi.org/10.7717/peerj.11250)
- Toward a more temporally explicit framework for community ecology
- Cross-sectional vs. longitudinal research: a case study of trees with hollows and marsupials in Australian forests
- Measuring continuous compositional change using decline and decay in zeta diversity
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Causal Effect Estimation
- **CMMB** - Sohn - [A compositional mediation model for a binary outcome: Application to microbiome studies](https://doi.org/10.1093/bioinformatics/btab605)
- **SparseMCMM_HD** - - [A microbial causal mediation analytic tool for health disparity and applications in body mass index](https://doi.org/10.21203/rs.3.rs-2463503/v1)
- Causal mediation analysis for longitudinal data with exogenous exposure
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Longitudinal Multi-omics Integration
- **timeOmics** - Bodein - [A Generic Multivariate Framework for the Integration of Microbiome Longitudinal Studies With Other Data Types](https://www.frontiersin.org/articles/10.3389/fgene.2019.00963) [vignette](http://www.bioconductor.org/packages/release/bioc/vignettes/timeOmics/inst/doc/vignette.html)
- **DIABLO** - Singh - Multi-block Sparse PLS-Discriminant Analysis - [DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays](https://doi.org/10.1093/bioinformatics/bty1054)
- **PALMO** - Vasaikar - [A comprehensive platform for analyzing longitudinal multi-omics data](https://doi.org/10.1038/s41467-023-37432-w)
- **PyIOmica** - Domanskyi - [PyIOmica: longitudinal omics analysis and trend identification](https://doi.org/10.1093/bioinformatics/btz896)
- **MEFISTO** - Velten - [Identifying temporal and spatial patterns of variation from multi-modal data using MEFISTO](https://www.nature.com/articles/s41592-021-01343-9) - [vignette](https://biofam.github.io/MOFA2/tutorials.html)
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Data Simulation
- **MTIST** - Hussey - [The MTIST platform: a microbiome time series inference standardized test simulation, dataset, and scoring systems](https://doi.org/10.1101/2022.10.18.512783)
- **SimMiL** - Weaver & Hendricks - [SimMiL: Simulating Microbiome Longitudinal Data](https://doi.org/10.1101/2024.03.18.585571)
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Mixed Modeling
- **MaAsLin 2** - Mallick - [Multivariable association discovery in population-scale meta-omics studies](https://doi.org/10.1371/journal.pcbi.1009442) - [vignette](https://github.com/biobakery/biobakery/wiki/maaslin2)
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Multi-level Modeling
- **mixOmics** - Liquet - [A novel approach for biomarker selection and the integration of repeated measures experiments from two assays](https://doi.org/10.1186/1471-2105-13-325)
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Bayesian Modeling
- **BioMiCo** - Shafiei - [BioMiCo: a supervised Bayesian model for inference of microbial community structure](https://doi.org/10.1186/s40168-015-0073-x)
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Network Analysis
- **eLSA** - Xia - [Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates](https://doi.org/10.1186%2F1752-0509-5-S2-S15)
- Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities
- Constructing the Microbial Association Network from large-scale time series data using Granger causality
- Statistical significance approximation for local similarity analysis of dependent time series data
- Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis
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Phylogeny-based
- A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome
- A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome
- A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome
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Pathway Analysis
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Reviews / Evaluations / Opinion
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Data Simulation
- Dynamic modeling and network approaches for omics time course data
- Causal discovery for the microbiome - 0)
- Statistical Considerations in the Design and Analysis of Longitudinal Microbiome Studies
- A review on longitudinal data analysis with random forest
- Multivariate methods for testing hypotheses of temporal community dynamics
- Statistical challenges in longitudinal microbiome data analysis
- Statistical Considerations in the Design and Analysis of Longitudinal Microbiome Studies
- How longitudinal data can contribute to our understanding of host genetic effects on the gut microbiome
- Methodological Considerations in Longitudinal Analyses of Microbiome Data: A Comprehensive Review
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Longitudinal Multi-omics Integration
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Longitudinal/Repeated Measures Application Papers
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Longitudinal Multi-omics Integration
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Data Simulation
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Categories
Sub Categories
Data Simulation
14
Linear/Mixed Modeling
10
Longitudinal Multi-omics Integration
9
Machine Learning/Artificial Neural Networks (Deep Learning) Methods
7
Ecology Literature
5
Network Analysis
5
Spline Modeling
5
Causal Effect Estimation
3
Pathway Analysis
3
Phylogeny-based
3
Stochastic/Probabilistic Modeling
2
Mixed Modeling
1
Bayesian Modeling
1
Multi-level Modeling
1