AB✳

IV. THE INSTRUMENT CATALOGUE

Tools of inquiry.

Languages, methods, and environments for examining biological systems and building useful things.

I

Programming & Development

Programming languages and development tools

  • Python
  • R
  • Bash
  • Git
  • GitHub
  • HTML / CSS
  • JavaScript / TypeScript
  • React / Next.js
II

Comparative & Evolutionary Genomics

Software used in comparative and evolutionary workflows

  • OrthoFinder
  • MAFFT
  • MUSCLE
  • IQ-TREE
  • PAML / codeml
  • ParaAT
  • CAFE5
  • BLAST+
III

Single-Cell Bioinformatics

Software and analytical methods for transcriptomic data

  • Seurat
  • Harmony
  • Quality control and normalization
  • PCA / UMAP
  • Cell clustering
  • Cell-type annotation
  • Marker-gene analysis
  • Differential expression
IV

RNA Sequencing

Tools for RNA-seq quality control, alignment, counting, and analysis

  • FastQC
  • fastp
  • MultiQC
  • STAR
  • HTSeq
  • DESeq2
  • Samtools
V

Scientific Computing

Computational environments and reproducible workflows

  • Linux
  • SLURM
  • High-performance computing
  • Conda
  • Reproducible workflow development
VI

Data Analysis & Statistics

Libraries and statistical methods

  • Pandas
  • Biopython
  • Data preprocessing
  • Chi-square goodness-of-fit tests
  • Standardized residual analysis
  • RSCU
  • ENC–GC3 analysis
  • Scientific visualization
  • Gene-expression analysis

A catalogue of tools and areas of practice. Project pages provide context as specific workflows are documented.