Repo_skeleton

Repo_skeleton contains default notebooks (project documenattion file structure) to copy over to a new repo.

Notebook Templates

Here’s a categorised list of common bioinformatics analysis pipelines, for which we provide template repos.

Genomics

ready	template notebook	description
[ ]	notebook_genome_assembly/	de novo genome assembly from long or short reads
[ ]	notebook_genome_annotation/	structural and functional genome annotation
[ ]	notebook_wgs/	whole genome resequencing analysis pipeline
[ ]	notebook_wes/	whole exome sequencing pipeline
[ ]	notebook_pan_genome/	construction and analysis of pan-genomes from multiple genomes
[ ]	notebook_structural_variant/	detection and analysis of large structural variants and CNVs (copy number variants)

Transcriptomics

ready	template notebook	description
[x]	notebook_bulk_rnaseq/	differential expression analysis of bulk RNA-Seq data
[ ]	notebook_total_rnaseq/	total rnaseq including non-coding and ribo-depleted data
[ ]	notebook_small_rnaseq/	analysis of small RNAs such as miRNAs and piRNA
[ ]	notebook_singlecell_rnaseq/	(single-cell) scRNA-seq clustering, annotation and visualization
[ ]	notebook_transcriptome_assembly/	de novo transcript reconstruction from RNA-Seq reads
[ ]	notebook_alternative_splicing/	detection and quantification of alternative splicing events

Epigenomics & Regulatory

ready	template notebook	description
[ ]	notebook_chip_seq/	transcription factor or histone ChIP-seq analysis
[ ]	notebook_atac_seq/	analysis of chromatin accessibility using ATAC-seq
[ ]	notebook_methylation_seq/	bisulfite sequencing or array-based dna methylation analysis
[ ]	notebook_hic/	genome-wide chromatin interaction analysis using Hi-C
[ ]	notebook_regulatory_landscape/	integration of ChIP, ATAC and RNA-Seq for regulatory element mapping

Microbiome & Metagenomics

ready	template notebook	description
[ ]	notebook_16s/	amplicon-based microbiome profiling using 16S rRNA
[ ]	notebook_metagenomics/	shotgun metagenome analysis including taxonomy and function
[ ]	notebook_metatranscriptomics/	expression profiling of microbial communities from RNA
[ ]	notebook_mag_reconstruction/	binning and annotation of metagenome-assembled genomes

Functional & Comparative

ready	template notebook	description
[ ]	notebook_functional_enrichment/	GO, KEGG or Pfam-based pathway and functional enrichment
[ ]	notebook_synteny/	comparative genome alignment and synteny block analysis
[ ]	notebook_phylogenomics/	phylogenetic tree construction from genome-scale data

Proteomics

ready	template notebook	description
[ ]	notebook_proteomics/	identification and quantification of proteins from LC-MS/MS data
[ ]	notebook_phosphoproteomics/	analysis of post-translational modifications (PTMs) like phosphorylation

Specialized & Advanced

ready	template notebook	description
[ ]	notebook_crispr_screen/	analysis of CRISPR pooled screens and gene knockout studies
[ ]	notebook_clinical_genomics/	variant interpretation using clinical and pathogenicity guidelines
[ ]	notebook_qtl_mapping/	discovery of eQTLs, sQTLs or methylation QTLs
[ ]	notebook_bulk_deconvolution/	estimation of cell-type proportions from bulk RNA-Seq
[ ]	notebook_multi_omics/	integration of transcriptomic, epigenomic and proteomic data