💻 Software & Environment Setup
Bioinformatics & Computational Biology
The computational toolchain and environment used throughout AI for Quantitative Pathology and Biomarker Analysis.
Digital pathology training for researchersQuantitative pathology biomarker for PhD studentsQuantitative pathology biomarker certificationQuantitative pathology biomarker training GermanyQuantitative pathology biomarker online workshopHistopathology training for researchers
# Recommended conda environmentconda create -n dstc_env python=3.11 -yconda activate dstc_envpip install biopython pandas pysam scikit-bioBiopython
Sequence I/O, BLAST parsing, phylogenetics
Sequence I/O, BLAST parsing, phylogenetics
SAMtools / BCFtools
Alignment & variant file manipulation
Alignment & variant file manipulation
Bioconductor (R)
DESeq2, edgeR & limma for expression analysis
DESeq2, edgeR & limma for expression analysis
Nextflow
Reproducible, portable NGS pipelines
Reproducible, portable NGS pipelines
Supported OS: Linux (Ubuntu 22.04+), macOS, or Windows via WSL2.
Hardware: 16 GB RAM minimum; a CUDA GPU helps for deep-learning modules.
Earn government-registered certification in AI for Quantitative Pathology and Biomarker Analysis
e-Certificate and e-Marksheet issued on successful completion.
