LICENSE
README.md
pyproject.toml
src/bulk_rnaseq_pipeline.egg-info/PKG-INFO
src/bulk_rnaseq_pipeline.egg-info/SOURCES.txt
src/bulk_rnaseq_pipeline.egg-info/dependency_links.txt
src/bulk_rnaseq_pipeline.egg-info/entry_points.txt
src/bulk_rnaseq_pipeline.egg-info/requires.txt
src/bulk_rnaseq_pipeline.egg-info/top_level.txt
src/rnaseq_pipeline/__init__.py
src/rnaseq_pipeline/__main__.py
src/rnaseq_pipeline/alignment.py
src/rnaseq_pipeline/bam_manager.py
src/rnaseq_pipeline/checkpoint.py
src/rnaseq_pipeline/cli.py
src/rnaseq_pipeline/config.py
src/rnaseq_pipeline/count_matrix.py
src/rnaseq_pipeline/data_manager.py
src/rnaseq_pipeline/dependency_manager.py
src/rnaseq_pipeline/design.py
src/rnaseq_pipeline/doctor.py
src/rnaseq_pipeline/ena_manager.py
src/rnaseq_pipeline/entrez.py
src/rnaseq_pipeline/environment_manager.py
src/rnaseq_pipeline/fastq_validator.py
src/rnaseq_pipeline/featurecounts.py
src/rnaseq_pipeline/geo_manager.py
src/rnaseq_pipeline/logger.py
src/rnaseq_pipeline/manifest.py
src/rnaseq_pipeline/net.py
src/rnaseq_pipeline/project.py
src/rnaseq_pipeline/project_health.py
src/rnaseq_pipeline/qc_manager.py
src/rnaseq_pipeline/quality_assessment.py
src/rnaseq_pipeline/r_bridge.py
src/rnaseq_pipeline/reference_manager.py
src/rnaseq_pipeline/report_manager.py
src/rnaseq_pipeline/runner.py
src/rnaseq_pipeline/secrets.py
src/rnaseq_pipeline/sra_manager.py
src/rnaseq_pipeline/storage.py
src/rnaseq_pipeline/strandedness.py
src/rnaseq_pipeline/stringtie.py
src/rnaseq_pipeline/system_check.py
src/rnaseq_pipeline/trimming.py
src/rnaseq_pipeline/ui.py
src/rnaseq_pipeline/validators.py
src/rnaseq_pipeline/workflow.py
src/rnaseq_pipeline/R/deseq2_pipeline.R
src/rnaseq_pipeline/R/differential_expression.R
src/rnaseq_pipeline/R/downstream_analysis.R
src/rnaseq_pipeline/R/qc_plots.R
src/rnaseq_pipeline/R/visualization.R
src/rnaseq_pipeline/config/default_config.yaml
src/rnaseq_pipeline/config/reference_catalog.yaml
src/rnaseq_pipeline/envs/rnaseq-r.yml
src/rnaseq_pipeline/envs/rnaseq-tools.yml