.gitignore
LICENSE
README.md
mkdocs.yml
pyproject.toml
.github/workflows/mkdocs.yml
.github/workflows/publish.yml
data/diann_dia/meta.csv
data/diann_dia/diann/report.parquet
data/sage_lfq/meta.csv
data/sage_lfq/sage/lfq.tsv
data/sage_lfq/sage/results.sage.tsv
data/sage_tmt/meta.csv
data/sage_tmt/sage/results.sage.tsv
data/sage_tmt/sage/tmt.tsv
docs/gen_ref_pages.py
docs/index.md
docs/installation.md
docs/nav.md
docs/requirements.txt
docs/assets/custom.css
docs/assets/favicon.ico
docs/assets/favicon.svg
docs/assets/fig1b.svg
docs/assets/icon.svg
docs/assets/logo.svg
docs/assets/overview.svg
docs/assets/images/visualization_correlation_1.png
docs/assets/images/visualization_id_1.png
docs/assets/images/visualization_id_2.png
docs/assets/images/visualization_intensity_1.png
docs/assets/images/visualization_missingness_1.png
docs/assets/images/visualization_pca_1.png
docs/assets/images/visualization_upset_1.png
docs/assets/images/visualization_var_1.png
docs/assets/images/visualization_var_2.png
docs/how-it-works/batch_correction.md
docs/how-it-works/data.md
docs/how-it-works/dea.md
docs/how-it-works/filter.md
docs/how-it-works/inference.md
docs/how-it-works/normalization.md
docs/how-it-works/purity.md
docs/how-it-works/summarization.md
docs/how-it-works/visualization.md
docs/tutorials/dda-lfq.ipynb
docs/tutorials/dda-tmt.ipynb
docs/tutorials/dea.ipynb
docs/tutorials/dia-lfq.ipynb
docs/tutorials/flashlfq.ipynb
docs/tutorials/ptm.ipynb
docs/tutorials/quick_start.ipynb
docs/tutorials/2024_Fulcher/01_process_rna_data.ipynb
docs/tutorials/2024_Fulcher/02_process_protein_data.ipynb
docs/tutorials/2024_Fulcher/03_handle_multi-omics_data.ipynb
docs/tutorials/2024_Fulcher/Fig2B_WNN_UMAP.svg
docs/tutorials/2024_Fulcher/Fig2C_MOFA_R2.svg
docs/tutorials/2024_Fulcher/Fig2D_f2_prot.svg
docs/tutorials/2024_Fulcher/Fig2D_f2_rna.svg
docs/tutorials/2024_Fulcher/index.md
msmu/__init__.py
msmu/_version.py
msmu/logging_utils.py
msmu/msmu.py
msmu.egg-info/PKG-INFO
msmu.egg-info/SOURCES.txt
msmu.egg-info/dependency_links.txt
msmu.egg-info/requires.txt
msmu.egg-info/top_level.txt
msmu/_plotting/__init__.py
msmu/_plotting/_pdata.py
msmu/_plotting/_plots.py
msmu/_plotting/_ptypes.py
msmu/_plotting/_template.py
msmu/_plotting/_trace.py
msmu/_plotting/_utils.py
msmu/_preprocessing/__init__.py
msmu/_preprocessing/_filter.py
msmu/_preprocessing/_infer_protein.py
msmu/_preprocessing/_normalisation.py
msmu/_preprocessing/_normalise.py
msmu/_preprocessing/_summarisation.py
msmu/_preprocessing/_summarise.py
msmu/_read_write/__init__.py
msmu/_read_write/_base_reader.py
msmu/_read_write/_diann.py
msmu/_read_write/_export.py
msmu/_read_write/_fragpipe.py
msmu/_read_write/_maxquant.py
msmu/_read_write/_mdata_status.py
msmu/_read_write/_reader_registry.py
msmu/_read_write/_reader_utils.py
msmu/_read_write/_sage.py
msmu/_read_write/label_info.py
msmu/_statistics/__init__.py
msmu/_statistics/_de_base.py
msmu/_statistics/_multiple_test_correction.py
msmu/_statistics/_permutation.py
msmu/_statistics/_statistics.py
msmu/_statistics/_target_decoy_q.py
msmu/_tools/__init__.py
msmu/_tools/_dea.py
msmu/_tools/_pca.py
msmu/_tools/_precursor_purity.py
msmu/_tools/_umap.py
msmu/_utils/__init__.py
msmu/_utils/fasta.py
msmu/_utils/get.py
msmu/_utils/peptide.py
msmu/_utils/protein.py
msmu/_utils/subset.py
msmu/_utils/utils.py
tests/conftest.py
tests/test_plotting_pdata.py
tests/test_plotting_plots.py
tests/test_plotting_template.py
tests/test_plotting_trace_ptypes.py
tests/test_plotting_utils.py
tests/test_preprocessing_filter.py
tests/test_preprocessing_infer_protein.py
tests/test_preprocessing_normalisation.py
tests/test_preprocessing_normalise.py
tests/test_preprocessing_summarisation.py
tests/test_read_write_base_reader.py
tests/test_read_write_export.py
tests/test_read_write_parsers.py
tests/test_read_write_reader_utils.py
tests/test_statistics_multiple_test_correction.py
tests/test_statistics_permutation_storey.py
tests/test_statistics_statistics.py
tests/test_statistics_target_decoy_q.py
tests/test_tools_dea_edge_cases.py
tests/test_tools_pca_umap_dea.py
tests/test_utils_fasta.py
tests/test_utils_helpers.py