RAINBio - Bioinformatics cloud appliances

Catalog of bioinformatics cloud appliances, which you can browse and filter according to the predefined keywords of the EDAM ontology or with natural language.

AnalysesSV
 

 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
 Francois Sabot Southgreen
ANF MetaBioDiv
 

 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
 Marc GAREL ANF MetaBioDiv
Askomics
 

 AskOmics
 Data integration and warehousing, Data visualisation
 olivier sallou GenOuest
BactComparativeGenomics
 

 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
 Alexis DEREEPER PHIM
Bacterial Genomics
 

 HMMER, Insygth, SGE - GridEngine, Ubuntu, Web interface
 Protein folds and structural domains, Sequence comparison, Sequence composition, complexity and repeats, Sequence sites, features and motifs, Genome annotation, Genomics, Informatics, Comparative genomics, Data visualisation, Function analysis, Gene and protein families
 Thomas Lacroix, StatInfOmics
Bioimage
 

 Bureau virtuel, Icy, ImageJ-Fiji, X2Go, XFCE
 Informatics, Data visualisation, Imaging
 Support Cloud IFB
BioPipes
 

 bioconda, cwltool, Docker, Nextflow, Snakemake
 Informatics, Bioinformatics, Workflows
 Support Cloud IFB
bistar
 

 bioconda, Bowtie2, FastQC, Snakemake
 Bioinformatics, Genomics, Mapping, Sequence alignment, Data quality management, Sequencing, Workflows, Sequence analysis
 aurelien beliard ICM-ICONICS
CentOS 7
 

 Ansible, bioconda, Docker
 Informatics, Bioinformatics
 Support Cloud IFB
CentOS 7 Desktop
 

 Ansible, bioconda, Bureau virtuel, Docker
 Informatics, Bioinformatics
 Support Cloud IFB
CoursAnalysesNanoporeSG
 

 bandage, Jupyter
 Data architecture, analysis and design, Mathematics, Statistics and probability, DNA structural variation, Sequence analysis, Sequencing, Whole genome sequencing, Genomics, Sequence assembly
 Francois Sabot - SouthGreen/IRD
Cytoscape
 

 Bureau virtuel, Cytoscape, X2Go, XFCE
 Bioinformatics, Data visualisation, Molecular interactions, pathways and networks, Informatics
 Support Cloud IFB
Debian 10
 

 Ansible, bioconda, Docker
 Bioinformatics, Informatics
 Support Cloud IFB
Debian 11
 

 Ansible, bioconda, Docker
 Bioinformatics, Informatics
 Support Cloud IFB
DRomics
 

 Bioconductor, DESeq2, DRomics, R - base, RStudio, Shiny
 Bioinformatics, Computational biology, Data management, Transcriptomics, Data visualisation, Data architecture, analysis and design, Statistics and probability
 Christophe Blanchet IFB-core
DRomicsInterpreter
 

 Bioconductor, DESeq2, DRomics, R - base, RStudio, Shiny
 Bioinformatics, Computational biology, Data management, Transcriptomics, Data visualisation, Data architecture, analysis and design, Statistics and probability
 Aurélie Siberchicot (aurelie.siberchicot@univ-lyon1.fr)
EBAME-2022 aDNA
 

 BAMtools, BEDTools, bioconda, Bowtie2, metaDMG-cpp, python3, SAMtools
 Data management, Bioinformatics, Sequence alignment, Computer science, Sequence analysis, Sequencing, Genomics, Mapping, Metagenomics, DNA mutation
 Lois Maignien, EBAME organization
EBAME-2022 MetaTOR
 

 Bowtie2, CheckM, hicstuff, Pairix, SAMtools
 Sequence alignment, Phylogenetics, Phylogenomics, Taxonomy, Imaging, Model organisms, Workflows, Sequence analysis, Sequencing, Genomics, DNA, Mapping, Microbial ecology, Sequence assembly, Metagenomics
 Martial Marbouty (Institut Pasteur)
EBAME-Anvio
 

 Anvi'o
 Genomics, Omics, Metagenomics, Phylogenomics, Transcriptomics
 Lois Maignien, EBAME organization
EBAME-Quince
 

 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
 Lois Maignien, EBAME organization
formation_CIRI
 

 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
 Marie CARIOU CIRI
Formation LBBE-NGS 2022
 

 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
 Stéphane Delmotte
frangiPANe
 

 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
 Christine TRANCHANT DIADE
Galaxy
 

 bioconda, Docker, Galaxy portal
 Informatics, Bioinformatics, Comparative genomics, Functional genomics, Genomics, Sequence assembly, Whole genome sequencing
 Support Cloud IFB
Genopole2019 GenomeVar
 

 bcftools, BEDTools, BWA, Canvas, FastQC, GATK, IGV - Integrative Genomics Viewer, IRSOM, Matplotlib, Numpy, pandas, plotnine, SAMtools, TensorFlow
 SNP, Data quality management, Informatics, Genetic variation, Genotyping experiment, GWAS study, Applied mathematics, Data visualisation, DNA polymorphism, Genomics, Mapping, Machine learning, Sequencing, Sequence analysis
 Vincent MEYER, CNRGH, CEA
GenopoleSchool Stats
 

 DESeq2, devtools (R), edgeR, FactoMineR, ggplot2, gridExtra, reshape2, RStudio, R - tidyverse, VennDiagram (R), Web interface
 Transcriptomics, ChIP-seq, Genetics, RNA-Seq, Data mining, Data architecture, analysis and design, Statistics and probability, Data visualisation
 Guillem RIGAILL, Inrae
integron_finder
 

 HMMER, Infernal, prodigal
 Protein folds and structural domains, Sequence comparison, Sequence composition, complexity and repeats, Sequence sites, features and motifs, Sequence analysis
 Bertrand Néron C3BI
Jupyter
 

 Julia, Jupyter, R - base
 Computer science, Mathematics, Data architecture, analysis and design, Data visualisation, Statistics and probability
 Support Cloud IFB
Kissplice-training
 

 Bioconductor, KisSplice, STAR
 Bioinformatics, Computational biology, Data management, Statistics and probability, Sequence assembly, Transcriptomics, RNA-Seq
 Stephane Delmotte stephane.delmotte@univ-lyon1.fr
lbbe-amc
 

 
 Data mining, Data visualisation, Statistics and probability
 Stephane Delmotte LBBE
LBMC Unix 2022
 

 Docker, Web interface
 Computer science
 Laurent Modolo laurent.modolo@ens-lyon.fr
M2BINF UCBL
 

 ete3, Jupyter
 Mathematics, Statistics and probability, Data visualisation, Phylogenomics, Data architecture, analysis and design
 Guillaume Launay, Université Claude Bernard Lyon 1 (Environnement pédagogique)
Metabarcoding_NFcore
 

 Jupyter, Matplotlib, Nextflow, pandas
 Data architecture, analysis and design, Mathematics, Statistics and probability, Workflows, Informatics
 Alexis DEREEPER BactPanGenomics
Mondrian
 

 Mondrian, R - base, Shiny
 Data architecture, analysis and design, Data visualisation, Statistics and probability
 Christophe Blanchet IFB-core
NGSanalysisJupyter
 

 BEDTools, BWA, Jupyter, SAMtools
 Data architecture, analysis and design, Mathematics, Statistics and probability, Sequence analysis, Sequencing, Bioinformatics, DNA polymorphism, DNA structural variation, Genomics, Mapping
 Francois Sabot DIADE
NGSgenotyp
 

 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
 Mathieu GENETE, EEP CNRS UMR8198
NMRProcFlow
 

 NMRProcFlow
 Metabolomics
 Daniel Jacob INRA
PlaScope
 

 Centrifuge, PlaScope, SPAdes
 Metagenomics, Sequence analysis, Genomics, Microbiology, Sequence assembly
 Mathieu Dubois email
REPET
 

 Repet
 Bioinformatics
 Hadi Quesneville URGI
RNASeq_SG
 

 FastQC, SAMtools, STAR
 Data quality management, Sequence analysis, Sequencing, RNA, Mapping, RNA-Seq, Transcriptomics
 Gautier SARAH RNA-Seq SG
Rocky Linux 8
 

 Ansible, bioconda, Docker
 Bioinformatics
 Support Cloud IFB
Rocky Linux 8 Desktop
 

 Ansible, bioconda, Bureau virtuel, Docker
 Bioinformatics
 Support Cloud IFB
Rstudio Génomique
 

 DESeq2, MMseqs2, RStudio, Web interface
 Transcriptomics, Sequence analysis, Sequence assembly, Data architecture, analysis and design, Data visualisation
 Stephane Delmotte
RStudio Server
 

 Bioconductor, R - base, RStudio, Web interface
 Computer science, Mathematics, Bioinformatics, Computational biology, Data management, Data architecture, analysis and design, Statistics and probability, Data visualisation
 Support Cloud IFB
SGE cluster
 

 SGE - GridEngine, Ubuntu
 Informatics
 Support Cloud IFB
Shiny
 

 R - base, R - tidyverse, Shiny, Web interface
 Data architecture, analysis and design, Bioinformatics, Data visualisation, Statistics and probability
 Support Cloud IFB
Ubuntu 18.04
 

 Ansible, bioconda, Docker
 Bioinformatics, Informatics
 Support Cloud IFB
Ubuntu 18.04 Desktop
 

 Ansible, bioconda, Bureau virtuel, Docker, X2Go, XFCE
 Bioinformatics, Informatics
 Support Cloud IFB
Ubuntu 20.04
 

 Ansible, bioconda, Docker
 Bioinformatics
 Support Cloud IFB
Ubuntu 20.04 Desktop
 

 Ansible, bioconda, Bureau virtuel, Docker, X2Go, XFCE
 Informatics, Bioinformatics
 Support Cloud IFB
Ubuntu 22.04
 

 Ansible, bioconda, Docker
 Bioinformatics
 Support Cloud IFB
Ubuntu 22.04 Desktop
 

 Ansible, bioconda, Bureau virtuel, Docker, X2Go, XFCE
 Informatics, Bioinformatics
 Support Cloud IFB
UE NGS-ENS Lyon
 

 BEDTools, Bowtie, Bowtie2, cmake, R - base, SAMtools
 Sequence alignment, Informatics, Data visualisation, Statistics and probability, Sequencing, Mapping, RNA-Seq, Transcriptomics, Sequence analysis, Genomics
 Carine Rey, Laboratoire de Biologie et Modélisation de la Cellule
UMR454-formation16S
 

 dada2, DESeq2, ggplot2, phyloseq, rANOMALY, RStudio
 Genetic variation, Microbial ecology, Sequencing, Transcriptomics, Microbiology, Sequence analysis, Data architecture, analysis and design, Metagenomics, Data visualisation
 Philippe RUIZ (UMR454 MEDIS)
VirtualRepeats
 

 BEDTools, RepeatMasker, RepeatModeler, Repet
 Genome annotation, Mobile genetic elements, Model organisms, Sequence assembly, Whole genome sequencing, Genomics, Sequence composition, complexity and repeats, Bioinformatics
 Florian Maumus bioinfo_te_2020
virus_ONT
 

 Jupyter
 Data architecture, analysis and design, Mathematics, Statistics and probability, Metagenomics, Sequence analysis
 Julie ORJUELA DIADE-IRD
WellInverter
 

 python3, Web interface, WellInverter
 Computer science, Bioinformatics, Gene regulation, Transcription factors and regulatory sites
 Hidde de Jong
Note that the color code has no meaning other than being constant for a given appliance.

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