LICENSE
MANIFEST.in
README.md
pyproject.toml
pranomics/__init__.py
pranomics/cli.py
pranomics/environment.py
pranomics/pipeline.py
pranomics.egg-info/PKG-INFO
pranomics.egg-info/SOURCES.txt
pranomics.egg-info/dependency_links.txt
pranomics.egg-info/entry_points.txt
pranomics.egg-info/requires.txt
pranomics.egg-info/top_level.txt
pranomics/modules/__init__.py
pranomics/modules/ai_interpretation.py
pranomics/modules/alignment.py
pranomics/modules/bam_processing.py
pranomics/modules/count_matrix.py
pranomics/modules/deg.py
pranomics/modules/deg_summary.py
pranomics/modules/differential_expression.py
pranomics/modules/fastq.py
pranomics/modules/fastqc.py
pranomics/modules/final_report.py
pranomics/modules/gene_annotation.py
pranomics/modules/gff_annotation.py
pranomics/modules/heatmap.py
pranomics/modules/html_report.py
pranomics/modules/interactive_plotly.py
pranomics/modules/pca.py
pranomics/modules/sample_discovery.py
pranomics/modules/sorting.py
pranomics/modules/stringtie_module.py
pranomics/modules/trimming.py
pranomics/modules/volcano.py
pranomics/utils/UI.py
pranomics/utils/__init__.py
pranomics/utils/checkpoint.py
pranomics/utils/conda_bootstrap.py
pranomics/utils/executor.py
pranomics/utils/flow.py
pranomics/utils/metadata_discovery.py
pranomics/utils/paths.py
pranomics/utils/reference_manager.py
pranomics/utils/report_engine.py
pranomics/utils/sample_discovery.py
pranomics/utils/state_manager.py
pranomics/utils/tool_manager.py
pranomics/utils/validators.py
scripts/edgeR_analysis.R
scripts/heatmap.R
scripts/pca.R
scripts/volcano.R