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Tools for researchers
who are stuck right now

Cheat sheets, checklists, video walkthroughs, and installation guides. Most are completely free — no email required.

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Your research needs a clearer route.

The Bioinformatics Roadmap turns an overwhelming field into a practical, publication-focused plan — from identifying the right question to producing results you can defend.

01Choose an analysis path that fits your biological question
02Understand the essential tools, data types, and decision points
03Build a research workflow that leads towards publication

The Bioinformatics Roadmap

A practical guide for researchers who want to move from data to defensible results.

OMIXLAB · RESEARCH EDITION

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Downloads

Cheat sheets & checklists

Most downloaded
PDF
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GWAS beginner checklist

The exact QC and analysis checklist used in population genomics studies — condensed to 2 pages.

  • Sample QC thresholds (call rate, heterozygosity)
  • SNP QC filters (MAF, HWE, LD pruning)
  • Population stratification steps
  • Association testing parameters
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Popular
PDF
Free — no email required

scRNA-seq pipeline cheat sheet

Every step from raw counts matrix to trajectory inference — on one printable page.

  • QC metrics and thresholds
  • Normalisation and feature selection
  • Dimensionality reduction (PCA, UMAP, tSNE)
  • Seurat and Scanpy function reference
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New
PDF
Free with email

Bioinformatics ebook: Dataset to Publication

40-page guide covering the full workflow — raw data to publication figures. Methods section template included.

  • How to audit a raw dataset before analysis
  • Choosing the right tool for your question
  • Methods section template included
Email requiredGet ebook →
Tool guide
PDF
Free — no email required

Linux command reference for bioinformatics

The 40 bash commands every bioinformatician actually uses — with real pipeline examples.

  • File and directory management
  • grep, awk, sed for parsing biological data
  • Conda environment management
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Tool guide
PDF
Free — no email required

GROMACS .mdp parameter reference

Key parameters for energy minimisation, NVT, NPT, and production runs with recommended starting values.

  • Energy minimisation parameter set
  • NVT/NPT equilibration templates
  • Production run parameter set
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Career
PDF
Free with email

Bioinformatics methods section template

Fill-in-the-blank templates for GWAS, scRNA-seq, variant calling, and molecular docking studies.

  • GWAS, scRNA-seq, variant calling templates
  • Molecular docking methods template
Email requiredGet template →
YouTube

Free video guides

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18:42
Install Ubuntu for bioinformatics (2025)

Dual boot, partition sizing, post-install config.

24:15
PLINK GWAS pipeline step by step

QC, stratification, association, Manhattan plot in R.

31:08
scRNA-seq QC in Seurat — the right way

Why default thresholds fail and how to set your own.

22:30
AutoDock Vina docking from scratch

PDB download to binding pose interpretation.

Installation guides

Every tool, installed correctly

PLK
PLINK 1.9 / 2.0
GWAS analysis toolkit
Guide →
GTK
GATK4
Variant calling pipeline
Guide →
GMX
GROMACS
MD simulation engine
Guide →
SRT
Seurat (R)
scRNA-seq analysis in R
Guide →
SCP
Scanpy (Python)
scRNA-seq in Python
Guide →
ADV
AutoDock Vina
Molecular docking
Guide →
BWA
BWA-MEM
Sequence alignment
Guide →
VMD
VMD + PyMOL
Molecular visualisation
Guide →