Pipeline Pool
Published PluMA pipelines
A curated collection of 109 pipelines assembled from PluMA
plugins, with peer-reviewed citations where applicable. Clone any pipeline from the pipelines/ directory of the PluMA source
tree.
- ABR Completed & Released
Antibiotic Resistance (Stebliankin et al, 2022)
movingpictures83/ABR - ADHD Completed & Released
ADHD 16S gut microbiome analysis (Cickovski et al, 2023)
movingpictures83/ADHD - Alpha1 Completed & Released
Alpha-1 Antitrypsin Deficiency multiomics analysis (Cickovski et al, 2019)
movingpictures83/Alpha1 - Alpine Completed & Released
Transcript abundance estimation by modeling RNAseq fragment bias (Love et al, 2016)
movingpictures83/Alpine - AmpliconHunter2 Completed & Released
High-performance amplicon prediction across multiple genome databases (Howard-Stone et al, 2026)
movingpictures83/AmpliconHunter2 - AmpliconNoise Completed & Released
Remove noise from 454 amplicons (Quince et al, 2011)
movingpictures83/AmpliconNoise - AmpliQue Completed & Released
Bacterial identification using 16S primer data (Gonzalez et al, 2008)
movingpictures83/AmpliQue - AMR Completed & Released
Antimicrobial resistance (Steblinakin et al, 2022)
movingpictures83/AMR - Antibiotics Completed & Released
Influence of antibiotics on bacterial growth (Stebliankin et al, 2021)
movingpictures83/Antibiotics - ASV Completed & Released
Convert raw metagenomics data to Amplicon Sequence Variants (ASVs) (Callahan et al, 2017)
movingpictures83/ASV - BacterialGrowth Completed & Released
Bacterial growth using peak-to-trough ratio (Stebliankin et al, 2020)
movingpictures83/BacterialGrowth - Bayes Completed & Released
Bayesian network (Auguet et al, 2021)
movingpictures83/Bayes - BaySeq Completed & Released
Empirical Bayesian methods for identifying differential expression (Hardcastle et al, 2010)
movingpictures83/BaySeq - BEDTools Completed & Released
BEDTools (Quinlan et al, 2010)
movingpictures83/BEDTools - Benchmark Completed & Released
Challenges in benchmarking metagenomic profilers (Sun et al, 2021)
movingpictures83/Benchmark - BRENDA Completed & Released
Multiomics analysis using the BRENDA (Casero-Cheema et al, 2017) enzyme database
movingpictures83/BRENDA - Cache Completed & Released
Machine learning and cache block replacement (Yusuf et al, 2021)
movingpictures83/Cache - Cancer Completed & Released
Pangenome cancer genome analysis (Poore et al, 2020)
movingpictures83/Cancer - CaReT Completed & Released
Classification And REgression Training (Kuhn et al, 2019)
movingpictures83/CaReT - Causality Completed & Released
Compute causal networks from microbiome abundance data (Sazal et al, 2019)
movingpictures83/Causality - CIC Completed & Released
Impact of "Best Practices" in the classroom (Cickovski et al, 2026)
movingpictures83/CIC - CoDiCast Completed & Released
Conditional Diffusion Model for Weather Prediction with Uncertainty Quantification (Shi et al, 2024)
movingpictures83/CoDiCast - Cohort Completed & Released
IHMP Cohort Analysis (Mathee et al, 2027)
movingpictures83/Cohort - COVID19 Completed & Released
Molecular mimicry with Covid-19 Spike protein (Nunez-Castilla et al, 2022)
movingpictures83/COVID19 - CQN Completed & Released
Conditional Quantile Normalization Method for RNA-Seq (Hansen et al, 2012)
movingpictures83/CQN - CysticFibrosis Completed & Released
16SrRNA variable regions, cystic fibrosis study (Doud et al, 2010)
movingpictures83/CysticFibrosis - DBN Completed & Released
Build a Dynamic Bayesian Network from longitudinal microbiome data (Ruiz-Perez et al, 2019)
movingpictures83/DBN - DEGSeq Completed & Released
Identify Differentially Expressed Genes from RNASeq data (Wang et al, 2010)
movingpictures83/DEGSeq - Derfinder Completed & Released
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution (Collado-Torres et al, 2017)
movingpictures83/Derfinder - DL_WaLeF Completed & Released
Deep Learning Models for Flood Predictions in South Florida (Shi et al, 2023)
movingpictures83/DL_WaLeF - DRIMSeq Completed & Released
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq (Nowicka and Robinson, 2016)
movingpictures83/DRIMSeq - EBSeq Completed & Released
Empirical Bayes Differential Expression analysis at both gene and isoform level using RNA-seq data (Ma et al, 2024)
movingpictures83/EBSeq - Electricity Completed & Released
Apply transformers to predict electricity consumption (Li et al 2020, Sama 2020)
movingpictures83/Electricity - EMoMiS Completed & Released
Epitope-based molecular mimicry search pipeline (Stebliankin et al, 2026)
movingpictures83/EMoMiS - Environment Completed & Released
Rubin causal model for estimating environmental exposure effects on microbiome (Sommer et al, 2021)
movingpictures83/Environment - Epitopedia Completed & Released
Identifying molecular mimicry between pathogens and known immune epitopes (Balbin et al, 2022)
movingpictures83/Epitopedia - FELLA Completed & Released
Interpretation and enrichment for metabolomics data (Picart-Armada et al, 2018)
movingpictures83/FELLA - FIDLAR Completed & Released
Forecast-Informed Deep Learning Architecture for Flood Mitigation (Shi et al, 2024)
movingpictures83/FIDLAR - Flint Completed & Released
Large-scale microbiome analysis in the cloud (Valdes et al, 2019)
movingpictures83/Flint - Flood Completed & Released
Flood prediction using machine learning (Shi et al, 2022)
movingpictures83/Flood - GAGE Completed & Released
Generally Applicable Gene-set Enrichment for Pathway Analysis (Luo et al, 2009)
movingpictures83/GAGE - Glutamine Completed & Released
Analysis of glutamine metabolite (Cickovski et al, 2021)
movingpictures83/Glutamine - GOExpress Completed & Released
Visualise microarray and RNAseq data using gene ontology annotations (Rue-Albrecht, 2024)
movingpictures83/GOExpress - GPU Completed & Released
Miscellaneous GPU-based pipelines using NVIDIA Kits (NVIDIA, 2016)
movingpictures83/GPU - GulfWar Completed & Released
Mouse Gulf War Illness study (Seth et al, 2022)
movingpictures83/GulfWar - HADDOCK Completed & Released
High Ambiguity Driven protein-protein DOCKing (Honorato et al, 2024)
movingpictures83/HADDOCK - HELIUS Completed & Released
Analysis of the HELIUS dataset (Nayman et al, 2023)
movingpictures83/HELIUS - HIVEvoNets Completed & Released
Evolutionary networks of sequence data and application to HIV (Buendia and Narasimhan, 2006)
movingpictures83/HIVEvoNets - IBD Completed & Released
Irritable Bowel Disorder (IBD) cohort analysis (Schreiner et al, 2026)
movingpictures83/IBD - Immunotherapy Completed & Released
Impact of immunotherapy on cancer microbiome (Stebliankin et al, 2019)
movingpictures83/Immunotherapy - InfantGut Completed & Released
Infant gut microbiome analysis (Ruiz-Perez et al, 2019)
movingpictures83/InfantGut - Jasper Completed & Released
Microbiome map assembly (Valdes et al, 2021)
movingpictures83/Jasper - Kaiju Completed & Released
Kaiju taxonomic classification (Menzel et al, 2016)
movingpictures83/Kaiju - Kidney Completed & Released
Kidney microbiome analysis (Park et al, 2020)
movingpictures83/Kidney - LipidQ Completed & Released
Lipidomics analysis pipeline (Nielsen et al, 2021)
movingpictures83/LipidQ - LSC Completed & Released
Improving PacBio Long Read Accuracy by Short Read Alignment (Au et al, 2012)
movingpictures83/LSC - MAPLE Completed & Released
MAPLE phylogenetic tree estimator (De Maio et al, 2025)
movingpictures83/MAPLE - MASH Completed & Released
Fast genome and metagenome distance estimation (Ondov et al, 2016)
movingpictures83/MASH - MathTest Completed & Released
Starter pipeline for PluMA, that performs basic arithmetic (Vargas, 2022)
rafaelcvargas22/MathTest - MeRRCI Completed & Released
Metagenome, Resistome, Replicome for Causal Inferencing (Stebliankin et al, 2022)
movingpictures83/MeRRCI - Metabolomics Completed & Released
Metabolomics pipeline (Stebliankin et al, 2022)
movingpictures83/Metabolomics - Metronidazole Completed & Released
Effect of metronidazole on vaginal microbiota (Ruiz-Perez et al, 2021)
movingpictures83/Metronidazole - MOSAIC Completed & Released
MOSAIC pipeline to compute Index of Replication (Stebliankin et al, 2020)
movingpictures83/MOSAIC - Mouse Completed & Released
Metagenomics pipeline to analyze 16S mouse gut microbiome data, from the PluMA userguide (Kozich et al, 2013)
movingpictures83/Mouse - MSN Completed & Released
Produce microbial social networks (Fernandez et al, 2015)
movingpictures83/MSN - OLego Completed & Released
OLego DeNovo mRNA splicing (Zhang et al, 2023)
movingpictures83/OLego - Opioid Completed & Released
Microbiome-related relationships between cocaine use and metabolites (Martinez et al, 2022)
movingpictures83/Opioid - OriginOfReplication Completed & Released
Compute the origin of replication (Brown et al, 2016)
movingpictures83/OriginOfReplication - OTU_ASV Completed & Released
OTU-ASV comparison on 16S cohort gut microbiome dataset (Nayman et al, 2022)
movingpictures83/OTU_ASV - PALM Completed & Released
Pipeline for the Analysis of Longitudinal Multi-omics time-series data (Ruiz-Perez et al, 2021)
movingpictures83/PALM - PanACEA Completed & Released
Pan-genome Atlas with Chromosome Explorer and Analyzer (Clarke et al, 2018)
movingpictures83/PanACEA - Parkinsons Completed & Released
16S gut microbiome dysbiosis in Parkinson's Disease patients (Pietrucci et al, 2019)
movingpictures83/Parkinsons - PCOS Completed & Released
Poly-Cystic Ovary Syndrome gut microbiome study (Menendez et al, 2026)
movingpictures83/PCOS - PetRI Completed & Released
PetRi pipeline for determining bacterial replication rates (Stebliankin et al, 2020)
movingpictures83/PetRI - PIsToN Completed & Released
Protein binding Interfaces with Transformer Networks (Stebliankin et al, 2023)
movingpictures83/PIsToN - Plots Completed & Released
Split a dataset, run compositional and differential analyses, compute correlations, produce plots (Aguilar-Pulido et al, 2015)
movingpictures83/Plots - PLSDASoYouThink Completed & Released
Partial Last Square Discriminant Analysis (PLSDA) Performance (Ruiz-Perez et al, 2020)
movingpictures83/PLSDASoYouThink - PM16S Completed & Released
Downstream 16S mouse gut microbiome analysis, pre- and post-obesity (Cickovski and Narasimhan, 2018)
movingpictures83/PM16S - PRADA Completed & Released
Prioritization of Regulatory Pathways based on Analysis of RNA Dynamics Alterations (Torres-Garcia et al, 2014)
movingpictures83/PRADA - PRIMAL Completed & Released
Pipeline for Retrieval of Interactions in the Microbiome from temporAL data (Lugo-Martinez et al, 2019)
movingpictures83/PRIMAL - ProcessAbund Completed & Released
Take raw abundances, normalize and threshold them, and split into groups (Riveros et al, 2014)
movingpictures83/ProcessAbund - Pseudomonas Completed & Released
Pseudomonas genome evolution (Rodriguez et al, 2027)
movingpictures83/Pseudomonas - PUMBA Completed & Released
Protein-protein interface evaluation with Vision Mamba (Shirali et al, 2026)
movingpictures83/PUMBA - Qiime2 Completed & Released
Qiime2 metagenomics pipeline (Polanco et al, 2020)
movingpictures83/Qiime2 - RAPToR Completed & Released
Resistome Abundance and Peak-to-Trough Ratio Pipeline (Stebliankin et al, 2022)
movingpictures83/RAPToR - RedTide Completed & Released
Gut microbiome analysis of red-tide microcystin exposed mice (Saha et al, 2022)
movingpictures83/RedTide - REPTILE Completed & Released
Regulatory DNA Element Prediction (He et al, 2016)
movingpictures83/REPTILE - RNASeq Completed & Released
Microbiome and host RNAseq pipeline (Jacobsen et al, 2025)
movingpictures83/RNASeq - RNASeqComp Completed & Released
Benchmarks for RNA-seq Quantification Pipelines (Teng et al, 2016)
movingpictures83/RNASeqComp - RNASeqReadSimulator Completed & Released
Produce synthetic RNA sequences with mutations (Li et al, 2013)
movingpictures83/RNASeqReadSimulator - SAHMI Completed & Released
Denoising sparse microbial signals from single-cell sequencing of mammalian host tissues (Ghaddar et al, 2022)
movingpictures83/SAHMI - Seurat Completed & Released
Single-Cell RNASeq Analysis (Hao et al, 2023)
movingpictures83/Seurat - SGSeq Completed & Released
Prediction and Quantification of Splice Events from RNA-Seq Data (Goldstein et al, 2014)
movingpictures83/SGSeq - SIDR Completed & Released
Sequence Identification with Decision tRees (Fierst and Murdock, 2017)
movingpictures83/SIDR - SINCERA Completed & Released
Single-Cell RNASeq Profiling (Guo et al, 2015)
movingpictures83/SINCERA - Smoking Completed & Released
Smoker 16S lung microbiome study (Campos et al, 2022)
movingpictures83/Smoking - Soil Completed & Released
Impact of heavy metal exposure on soil microbiome (Morales et al, 2027)
movingpictures83/Soil - SVA Completed & Released
Surrogate Variable Analysis (Leek et al, 2014)
movingpictures83/SVA - T2D Completed & Released
Type-2 Diabetes Mellitus (Nayman et al, 2024)
movingpictures83/T2D - Tara Completed & Released
Structure and function of the global ocean microbiome (Sunagawa et al, 2015)
movingpictures83/Tara - Tensorflow Completed & Released
Pipeline with miscellaneous Tensorflow utilities (Rodriguez and Riggs, 2016)
movingpictures83/Tensorflow - TGCN Completed & Released
Temporal Graph Convolutional Network for Traffic Prediction (Zhao et al, 2018)
movingpictures83/TGCN - Tuxedo Completed & Released
Differential gene and transcript expression analysis (Trapnell et al, 2012)
movingpictures83/Tuxedo - UMiami16S Completed & Released
16S pipeline, (Exercise, Duodenal Adenoma, Microbiota/Macrophage) with UMiami-FL (Burgueno et al, 2025)
movingpictures83/UMiami16S - Veg3CAMR Completed & Released
Antimicrobial resistance using 3C denovo assembly (Sakthivel et al, 2027)
movingpictures83/Veg3CAMR - Viral Completed & Released
Viral challenge (2016)
movingpictures83/Viral - VPhyloMM Completed & Released
Viral mutational pathways of drug resistance (Buendia et al, 2009)
movingpictures83/VPhyloMM - HGT In Progress
Using machine learning to detect Horizontal Gene Transfer (Spaulding et al, 2027)
movingpictures83/HGT - SynPDClassify Future
Parkinson's Case/Control Discrimination (Quinn et al, 2027)
quinnjr/SynPDClassify
Have a new pipeline to contribute? Send your repository and description to the project manager at FIU BioRG — see the official site for current contact information.