c(
person("Aaron", "Millan-Oropeza", email = "aaron.ibt@gmail.com", role = c("aut", "cre")),
person("Catherine", "Juste", email = "catherine.juste@inrae.fr", role = c("aut", "ctb")),
person("Ariane", "Bassignani", email = "ariane.bassignani@gmail.com", role = c("aut", "ctb")),
person("Céline", "Henry", email = "celine.henry@inrae.fr", role = c("aut", "ctb"))
)
Aaron Millan-Oropeza [aut, cre],
Catherine Juste [aut, ctb],
Ariane Bassignani [aut, ctb],
Céline Henry [aut, ctb]
Set of tools for descriptive analysis of metaproteomics data generated from high-throughput
mass spectrometry instruments. These tools allow to cluster peptides and proteins abundance,
expressed as spectral counts, and to manipulate them in groups of metaproteins. This information
can be represented using multiple visualization functions to portray the global metaproteome
landscape and to differentiate samples or conditions, in terms of abundance of metaproteins,
taxonomic levels and/or functional annotation. The provided tools allow to implement flexible
analytical pipelines that can be easily applied to studies interested in metaproteomics analysis.
ade4, dendextend, dplyr, ggforce, ggrepel, reshape2, stringr,
tidyverse

metafor (>= 1.9.9), lme4, numDeriv, BiasedUrn, knitr,
rmarkdown
User-friendly package for reporting replicability-analysis methods, affixed to meta-analyses summary. The replicability-analysis output provides an assessment of the investigated intervention, where it offers quantification of effect replicability and assessment of the consistency of findings.
- Replicability-analysis for fixed-effects and random-effect meta analysis:
- r(u)-value;
- lower bounds on the number of studies with replicated positive and\or negative effect;
- Allows detecting inconsistency of signals;
- forest plots with the summary of replicability analysis results;
- Allows Replicability-analysis with or without the common-effect assumption.

User-friendly package for reporting replicability-analysis methods, affixed to meta-analyses summary. This package implements the methods introduced in Jaljuli et. al. (2022) <doi:10.1080/19466315.2022.2050291>. The replicability-analysis output provides an assessment of the investigated intervention, where it offers quantification of effect replicability and assessment of the consistency of findings.
- Replicability-analysis for fixed-effects and random-effect meta analysis:
- r(u)-value;
- lower bounds on the number of studies with replicated positive and\or negative effect;
- Allows detecting inconsistency of signals;
- forest plots with the summary of replicability analysis results;
- Allows Replicability-analysis with or without the common-effect assumption.