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Environments |
Operating Systems |
Windows
Linux (Ubuntu and Debian) Oracle VM VirtualBox SLURM workload manager |
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Version control |
Conda
Anaconda
Singularity |
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Languages |
C++
JAVA
Python
BioPython
R
Perl
BioPerl
C
bash PHP HTML CSS JavaScript |
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Databases |
MySQL NoSQL PostgreSQL MongoDB | |
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FAIR |
GitHub GitLab Jupyter Markdown snakemake | |
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Tools |
Omics | ChromHMM MACS2 Bowtie FASTQC bedtools samtools deeptools Artemis Staden Pregap HOMER |
| Structural biology | PyMol Vina Autodock Chimera | |
| Phylogenetics | iTOL CheckM RAxML trimAl BLAST Sim4 MEGA ClustalW | |
| Visualisation | SeeView IGV UCSC Genome Browser | |
| Workflows | pipeline FROGS Galaxy | |
| Neurosciences | Neurons | |
| R packages | ClusterProfiler fastICA ggplot2 | |
| Python libraries | tkinter, matplotlib | |
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Public databases |
NCBI, Pfam, STRING, PROSITE, PANTHER, KEGG, Reactome, GTDB, SwissProt, InterPro, RCSB PDB API NCBI EUtilities, API REST, API MGnify |
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Analysis |
Genomics Epigenomics (ATAC-seq, ChIP-seq) Transcriptomics (RNA-seq and single-cell RNA-seq) Structural Biology and Molecular Modelling Machine learning, deep learning, neural networks, text mining Metagenomics Phylogenetics |
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Statistics |
Matrix factorisation : PCA, ICA, Clustering Linear and non linear regression, Markov models and HMM Functional Enrichment analyses (ORA & GSEA) |
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