Repo_skeleton contains default notebooks (project documenattion file structure) to copy over to a new repo.
Here’s a categorised list of common bioinformatics analysis pipelines, for which we provide template repos.
| 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) |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |