Appliance	Tools	Topics
Analycyte Latest	R - base R - tidyverse Shiny Web interface	Biomarkers Oncology Workflows Data visualisation Statistics and probability Data architecture, analysis and design
AnalysesSV 1.0	bcftools BEDTools BWA Jupyter Matplotlib pandas SAMtools	DNA polymorphism Genetic variation Genotyping experiment GWAS study SNP Genomics Data architecture, analysis and design Mathematics Statistics and probability Sequencing Mapping Informatics DNA structural variation Sequence analysis
ANF MetaBioDiv 1.0	Bioconductor DESeq2 devtools (R) ggplot2 gridExtra phyloseq reshape2 RStudio	Bioinformatics Computational biology Data management Transcriptomics Microbiology Statistics and probability Metagenomics Sequence analysis Data architecture, analysis and design Data visualisation
ANF OMERO-FAIRly 2023.06	bioconda CellProfiler Jupyter Matplotlib Numpy pandas python3	Microarray experiment Data architecture, analysis and design Mathematics Computer science Informatics Bioinformatics Genotype and phenotype Imaging Statistics and probability
Askomics 3.2	AskOmics	Data integration and warehousing Data visualisation
ateliersUARDoHNEE 1.0	BWA FastQC SAMtools SPAdes	Sequencing Mapping Sequence analysis Sequence assembly
BactComparativeGenomics 1.0	ImageJ2 Jupyter MACS2 Matplotlib Nextflow pandas Prokka	Imaging Mathematics Statistics and probability ChIP-seq Workflows Data architecture, analysis and design Informatics Gene expression RNAi experiment Genomics Sequence analysis
Bioimaging Desktop Latest	Bureau virtuel Icy ImageJ-Fiji MATE Napari OMERO.insight QuPath X2Go	Light microscopy Medical imaging Informatics Data visualisation Imaging
biom3d 1.0	Biom3d Bureau virtuel python3 X2Go XFCE	Informatics Bioinformatics Biology Biomedical science Computational biology Data visualisation Machine learning Software engineering Computer science
BioPipes latest	bioconda cwltool Docker Nextflow Snakemake	Informatics Bioinformatics Workflows
bistar 1.0	bioconda Bowtie2 FastQC Snakemake	Bioinformatics Genomics Mapping Sequence alignment Data quality management Sequencing Workflows Sequence analysis
CoursAnalysesNanoporeSG 1.0	bandage Jupyter	Data architecture, analysis and design Mathematics Statistics and probability DNA structural variation Sequence analysis Sequencing Whole genome sequencing Genomics Sequence assembly
Cytoscape Latest	Bureau virtuel Cytoscape X2Go XFCE	Informatics Bioinformatics Data visualisation Molecular interactions, pathways and networks
Debian 12 12	Ansible bioconda Docker	Bioinformatics Informatics
Debian 13 13	Ansible bioconda Docker	Bioinformatics Informatics
Decomics 1.0	Bioconductor ggplot2 Shiny	Bioinformatics Computational biology Data management Data architecture, analysis and design Gene expression Data visualisation Statistics and probability
DRomics latest	Bioconductor DESeq2 DRomics R - base Shiny	Bioinformatics Computational biology Data management Data visualisation Data architecture, analysis and design Transcriptomics Statistics and probability
DRomicsInterpreter latest	Bioconductor DESeq2 DRomics R - base RStudio Shiny	Bioinformatics Computational biology Data management Transcriptomics Data visualisation Data architecture, analysis and design Statistics and probability
EBAME-Anvio v8	Anvi'o	Genomics Omics Metagenomics Phylogenomics Transcriptomics
EBAME MetaTOR 2025-10	Bowtie2 CheckM hicstuff Pairix SAMtools	Sequence alignment Data quality management Phylogenetics Phylogenomics Taxonomy Imaging Model organisms Workflows Sequence analysis Sequencing Genomics DNA Mapping Microbial ecology Sequence assembly Metagenomics
EBAME-Quince 2024-10	bam-readcount BEDTools BWA CONCOCT DESeq2 Diamond Kraken MAFFT Matplotlib MEGAHIT prodigal R - base SAMtools SPAdes	Transcriptomics Informatics Sequencing Genomics Metagenomics Phylogenetics Bioinformatics Data visualisation Statistics and probability Sequence assembly Mapping Sequence analysis
ENSL-CPES-RNAseq 2025 0.1	BEDTools Bowtie2 DESeq2 edgeR HTSeq limma (R) Matplotlib Numpy pysam RStudio SAMtools Tophat	Sequence alignment ChIP-seq Molecular biology Data architecture, analysis and design Data visualisation Genetics Informatics Sequencing Mapping Transcriptomics RNA-Seq Sequence analysis Genomics
ETBII AnalyseMultivariée 1.1	BiocStyle ButchR clusterProfiler ComplexHeatmap DESeq2 DT (R) factoextra FactoMineR gage GGally ggupset MMseqs2 MOFA2 msigdbr RStudio umap viridis YAPSA	Literature and language Transcriptomics Sequence assembly Machine learning Statistics and probability Sequence analysis Genomics Data architecture, analysis and design Genetic variation Oncology Applied mathematics Genetics Data mining Molecular interactions, pathways and networks Data visualisation
ETBII Reseaux 1.1	BiNGO (Cytoscape) Bureau virtuel compositions (R) Cytoscape DESeq2 ecodist igraph MMseqs2 network Omics Visualizer (Cytoscape) RStudio SNFtool stringApp (Cytoscape) WGCNA X2Go XFCE yFiles Layout Algorithms (Cytoscape)	Transcriptomics Sequence analysis Sequence assembly Gene expression Rare diseases Informatics Functional genomics Bioinformatics Ecology Protein interactions Data architecture, analysis and design Molecular interactions, pathways and networks Data visualisation
formation_CIRI 1.0	DESeq2 FastQC HISAT2 RStudio Trimmomatic	Transcriptomics Whole genome sequencing Data architecture, analysis and design Data visualisation Data quality management Sequencing RNA-Seq Genomics Mapping Sequence analysis
Formation LBBE-NGS 2024 3.0	BEDTools Bioconductor DESeq2 HISAT2 IGV - Integrative Genomics Viewer SAMtools X2Go	Bioinformatics Computational biology Data management Statistics and probability Transcriptomics Whole genome sequencing Sequence analysis Sequencing Informatics Mapping Genomics
frangiPANe 1.0	ABySS bioPython BWA CD-HIT Docker Jupyter python3 SAMtools	Phylogenetics Population genetics Protein structure analysis Sequence alignment Sequence clustering Sequence comparison Data architecture, analysis and design Mathematics Statistics and probability Computer science Sequencing Sequence assembly Sequence analysis Mapping
génomique_environnement 1.0	Bioconductor BLAST Bowtie2 Cutadapt FastQC HMMER R - base	Computational biology Data management Sequence analysis Mapping Sequence alignment Protein folds and structural domains Sequence comparison Sequence composition, complexity and repeats Sequence sites, features and motifs Data visualisation Bioinformatics Statistics and probability Environmental science Genomics
integron_finder 1.5.1	HMMER Infernal prodigal	Protein folds and structural domains Sequence comparison Sequence composition, complexity and repeats Sequence sites, features and motifs Sequence analysis
Jupyter latest	Julia Jupyter R - base	Computer science Mathematics Computational biology Machine learning Workflows Data architecture, analysis and design Data visualisation Statistics and probability
Kissplice-training 1.0	Bioconductor KisSplice STAR	Bioinformatics Computational biology Data management Statistics and probability Sequence assembly Transcriptomics RNA-Seq
lbbe-amc 1.0		Data mining Data visualisation Statistics and probability
LBMC Unix 2022 1.0	Docker Web interface	Computer science
lr16s_ONT 1.0	Cutadapt EMU MultiQC NanoStat Porechop Porechop_ABI python3 R seqkit VSEARCH	Genotype and phenotype Population genetics Population genomics Statistics and probability Database management Metagenomics Sequencing Genomics Sequence analysis Marine biology Microbiology Computer science Bioinformatics
M2BINF UCBL 2024.03	ete3 Jupyter	Mathematics Statistics and probability Data visualisation Phylogenomics Data architecture, analysis and design
MAGNETO 1.4	ABRicate AMRFinderPlus bioconda Bowtie2 CheckM Cloud4SAMS [Project] CONCOCT CoverM EggNOG-mapper FastQ Screen fatsp geNomad GTDB-Tk MEGAHIT MetaBAT 2 MMseqs2 mOTUs MultiQC prodigal SemiBin Snakemake	Infectious disease Public health and epidemiology Mapping Sequence alignment Data quality management Phylogenomics Computational biology Data security Transcriptomics Probes and primers Database management Proteins Metagenomic sequencing Sequencing Machine learning Microbial ecology Phylogenetics Taxonomy Microbiology Sequence assembly Genomics Sequence analysis Workflows Bioinformatics Metagenomics
Metabarcoding_NFcore 1.0	Jupyter Matplotlib Nextflow pandas	Data architecture, analysis and design Mathematics Statistics and probability Workflows Informatics
Metabolic Modelling 2024-11	gapseq kegg2bipartitegraph MeneTools Metage2metabo MiSCoTo PADMet prodigal	Enzymes Genotype and phenotype Small molecules Data visualisation Sequence analysis Endocrinology and metabolism Molecular interactions, pathways and networks Metabolic pathways Microbial ecology Metabolomics Metagenomics
Mondrian 1.0	Mondrian R - base Shiny	Data architecture, analysis and design Data visualisation Statistics and probability
NGSanalysisJupyter 1.0	BEDTools BWA Jupyter SAMtools	Data architecture, analysis and design Mathematics Statistics and probability Sequence analysis Sequencing Bioinformatics DNA polymorphism DNA structural variation Genomics Mapping
NGSgenotyp 1.0	bioPython bowtie2 cap3 ete3 FastQC Matplotlib muscle Numpy phyml pysam python QUAST SAMtools Scipy SPAdes sratoolkit yass	Phylogenetics Protein structure analysis Data visualisation Phylogenomics Phylogeny Sequence analysis Genomics Mapping Informatics Sequencing Bioinformatics Genotype and phenotype Population genomics Population genetics Sequence assembly
NMRProcFlow 1.2.26	NMRProcFlow	Metabolomics
PlaScope 1.3.1	Centrifuge PlaScope SPAdes	Metagenomics Sequence analysis Genomics Microbiology Sequence assembly
REPET 3.0	Repet	Bioinformatics
RNASeq_SG 1.0	FastQC SAMtools STAR	Data quality management Sequence analysis Sequencing RNA Mapping RNA-Seq Transcriptomics
Rocky Linux 8 8	Ansible bioconda Docker	Bioinformatics Informatics
Rocky Linux 8 Desktop 8	Ansible bioconda Bureau virtuel Docker	Bioinformatics Informatics
Rocky Linux 9 9	Ansible bioconda Docker	Bioinformatics Informatics
Rocky Linux 9 Desktop 9	Ansible bioconda Bureau virtuel Docker	Bioinformatics Informatics
Rstudio Génomique 2.0	BEDTools dada2 DESeq2 HISAT2 IGV - Integrative Genomics Viewer Matplotlib MMseqs2 RStudio SAMtools Web interface	Genetic variation Metagenomics Microbial ecology Transcriptomics Whole genome sequencing Informatics Sequence assembly Sequencing Mapping Sequence analysis Genomics Data architecture, analysis and design Data visualisation
RStudio Server latest	Bioconductor R - base RStudio Web interface	Computer science Machine learning Mathematics Bioinformatics Computational biology Data management Data architecture, analysis and design Statistics and probability Data visualisation
Shaman 2023	R - base R - tidyverse Shaman Shiny	Statistics and probability Data architecture, analysis and design Bioinformatics Metagenomics Data visualisation
Shiny Latest	R - base R - tidyverse Shiny Web interface	Data architecture, analysis and design Bioinformatics Data visualisation Statistics and probability
ShIVA Latest	Shiny	Data architecture, analysis and design Statistics and probability Bioinformatics Data mining Data visualisation RNA-Seq Sequencing
Spatial-Cell-ID-Jupyter 1.0	Jupyter Matplotlib Napari Numpy pandas python3 Scipy	Data architecture, analysis and design Mathematics Computer science Informatics Statistics and probability Data visualisation Imaging
Ubuntu 22.04 22.04	Ansible bioconda Docker	Bioinformatics Informatics
Ubuntu 22.04 Desktop 22.04	Ansible bioconda Bureau virtuel Docker MATE X2Go	Bioinformatics Informatics
Ubuntu 24.04 24.04	Ansible bioconda Docker	Bioinformatics Informatics
Ubuntu 24.04 Desktop 24.04	Ansible bioconda Bureau virtuel Docker MATE X2Go	Bioinformatics Informatics
UE NGS-ENS Lyon 2026.1	BEDTools cmake DESeq2 R - base SAMtools STAR	Informatics Data visualisation Statistics and probability Mapping Sequencing Genomics Sequence analysis Transcriptomics RNA-Seq
UMR454-formation16S 1.0	dada2 DESeq2 ggplot2 phyloseq rANOMALY RStudio	Genetic variation Microbial ecology Sequencing Transcriptomics Microbiology Sequence analysis Data architecture, analysis and design Metagenomics Data visualisation
VirtualRepeats 0.1	BEDTools RepeatMasker RepeatModeler Repet	Genome annotation Mobile genetic elements Model organisms Sequence assembly Whole genome sequencing Genomics Sequence composition, complexity and repeats Bioinformatics
virus_ONT 1.0	Jupyter	Data architecture, analysis and design Mathematics Statistics and probability Metagenomics Sequence analysis
WellInverter 19.03	python3 Web interface WellInverter	Computer science Bioinformatics Gene regulation Transcription factors and regulatory sites

Appliances