| Sequencing & Pipelines | STAR, Salmon, BWA, Bowtie2, Cellranger, nf-core, Nextflow, Snakemake, Galaxy | Bulk RNAseq, single-cell, WGS, exome, ChIP-seq, ATAC-seq pipelines. |
| Single-Cell Analysis | Seurat, scanpy, scvi-tools, Bioconductor, Monocle3, scVelo, CellChat, CellRank | Single-cell clustering, integration, trajectory inference. |
| Statistics & Languages | R (tidyverse, lme4, brms), Python (pandas, scipy, statsmodels), Stata, GraphPad Prism, JASP | Mixed models, Bayesian inference, hypothesis testing. |
| Microscopy & Imaging | ImageJ/FIJI, CellProfiler, Ilastik, napari, Imaris, Huygens, CHIMERAX | Image segmentation, quantification, 3D rendering. |
| Genomics Databases | UCSC Genome Browser, Ensembl, NCBI, UniProt, ENCODE, GTEx, UK Biobank, gnomAD, ClinVar, dbSNP | Reference data, annotation, cross-validation. |
| CRISPR Tools | CRISPick, Benchling, Synthego, CRISPOR, MAGeCK, BAGEL2, ScreenPro2 | Guide design, screen analysis. |
| Structural Biology | AlphaFold 3, ColabFold, ChimeraX, PyMOL, VMD, GROMACS, AMBER | Structure prediction, MD simulation, drug-target interaction. |
| Phylogenetics | IQ-TREE, RAxML, MrBayes, BEAST2, MEGA-X, MAFFT, T-Coffee | Sequence alignment, tree inference, divergence dating. |
| Reproducibility | Nextflow, Snakemake, Conda, Docker / Apptainer, Git, Zenodo, FAIR DOME | Pipeline reproducibility and FAIR data deposition. |
| HPC & Cloud | ARCHER2, JADE2, Isambard-AI, AWS, GCP, Azure, Tier-2 clusters | Large-scale omics, simulations, ML workflows. |
| Reporting Standards | MIQE, MIAME, MINSEQE, ARRIVE 2.0, CONSORT, PRISMA, FAIR | Tighten each chapter to discipline-specific standards. |
| Target Journals | Nature, Cell, Science, eLife, PNAS, Nat Genet, Nat Methods, Genome Biology, EMBO J, JCB | Top-tier publication target alignment. |