Bioinformatics Code Hub

A community collection of bioinformatic analyses for anyone to learn and adapt.

Need help with an analysis? You can open an issue:

• Request a specific analysis
• Request an analysis expanded for your needs
• Request help with downloading/processing a specific dataset

Good at bioinformatics? Consider contributing your code!

Planned Analyses:

Genomics

• Copy-number variation
• Variant calling
  • Small variants (GATK)
  • Structural variants (Manta)
  • Haplotype phasing (WhatsHap)
• Variant annotation (VEP, ANNOVAR)
• GWAS
  • QC & imputation (PLINK, Eagle)
  • Association testing
• Population genetics
  • PCA / ADMIXTURE
  • Selection scans (iHS, Fst)

Transcriptomics

• Bulk RNA-seq
  • QC
  • Alignment
  • Differential expression:
    • DESeq2 - R
    • PyDESeq2
    • edgeR
  • Counts generation:
    • Kallisto
  • Isoform analysis (IsoformSwitchAnalyzeR)
  • Co-expression networks (WGCNA)
  • GSEA / pathway analysis
• Single-cell RNA-seq
  • Preprocessing (Cell Ranger / Alevin-fry)
  • Normalisation & batch correction (SCTransform / Harmony)
  • Doublet detection (Scrublet)
  • Clustering & visualisation
  • Cell-type annotation:
    • CellTypist
    • SingleR
    • scmap
  • Differential expression
  • TF analysis
  • Pseudotime / trajectory analysis
  • Ligand-receptor interactions
• Spatial transcriptomics
  • Visualize clusters and genes on spatial coordinates
  • Spot deconvolution (RCTD)
  • Image-based QC
• Long-read transcriptomics (Iso-seq, Nanopore)

Epigenomics

• DNA methylation
  • Illumina array (450k, 850k, EPIC)
• ATAC-seq / chromatin accessibility
• ChIP-seq
• Hi-C / 3D genome
• Single-cell epigenomics (snmC-seq, scATAC)

Proteomics

• LC-MS preprocessing (MaxQuant)
• Differential protein abundance
• PTM site localisation
• Spectral library generation
• Protein–protein interaction networks (STRING / Cytoscape)

Metabolomics

• LC-MS untargeted workflows (MS-Dial / XCMS)
• NMR spectroscopy
• Pathway mapping (Mummichog)

Metagenomics

• 16S/18S rRNA amplicon pipelines (QIIME 2)
• Shotgun metagenome assembly & binning (MetaBAT)
• Functional profiling (HUMAnN)

Structural Bioinformatics & Molecular Simulation

• Homology modelling (MODELLER)
• Docking (AutoDock Vina)
• Molecular dynamics
  • MDVerse
  • GROMACS
  • OpenMM

Imaging & Computer Vision

• Bright-field / fluorescence segmentation (Cellpose, Stardist)
• Cell tracking (DeepCell)
• Medical imaging (MRI, CT)

Machine Learning & Statistics

• ML for omics
• Deep learning (keras-tensor) for sequence data
• AutoML notebooks (auto-sklearn)

Multi-Omics Integration

• MOFA / DIABLO integrative analysis
• Network-based integration

Utilities & QC

• File-format conversions (BAM ⇆ CRAM)
• Reference genome downloads (NCBI, Ensembl)
• Workflow management (Snakemake, Nextflow)

Datasets used:

• Bulk RNA-Seq:
  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164073
• Single-cell RNA-Seq:
  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109816
• Spatial transcriptomics:
  • https://data.mendeley.com/datasets/mbvhhf8m62/2
• Transcriptomics:
  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE229677

Contributions are welcome ❤️

This project is licensed under the MIT License.