Bioinformatic workflows used in different fields of biology for educational and benchmarking purposes. This is and will stay a work in progress and we welcome any user to submit PRs to include their workflows.
List of bioinformatic benchmarks included in this repository.
| Benchmark name | Benchmark description |
| affy | Analysis of MicroArray data |
| clinical_eslII | Analysis of clinical data (according to book ESL 2nd edition) |
| clinical_livercohort | Analysis of clinical data from liver cohort study |
| generate_count | Generate count tables from RNAseq data |
| integration_igraph | Integerate different biological data with iGraph |
| integration_livercohort | Integrate data from liver cohort study with another data sourc |
| microarray | Analysis of microarray datasets |
| mutation | Analysis of SNP data |
| rnaseq_deseq2 | Analysis of RNAseq data using DESeq2 |
| rnaseq_preprocess | Preprocessing of RNAseq files to generate count data from FASTA files |
| rppa | Analysis of Reverse Phase Protein Array (RPPA) data |
| simulated_geo_matrix | Analysis of simulated gene expression and patient meta data |
| singlecell_seurat_mrkr_discov | Single cell gene expression analysis for marker discovery (using Seurat) |
| singlecell_seurat_spatial_infer | Single cell gene expression analysis for sepatial inference (using Seurat) |
| survival_simple | Simple survival analysis |
| survival_tcga | Survival analysis using TCGA data |
| tcga_browser | Modules used in a shiny app to visualize TCGA data |