Files in PelzKo/immunedeconv2
Second generation methods for immune cell deconvolution
.Rbuildignore
.gitattributes
.github/.gitignore
.github/workflows/pkgdown.yml
.github/workflows/roxygenize.yml
.github/workflows/test-coverage.yml
.github/workflows/test.yml
.gitignore
.pre-commit-config.yaml
CIBERSORT-Results.txt
DESCRIPTION
LICENSE
NAMESPACE
R/AutoGeneS.R
R/BSEQ_sc.R
R/BayesPrism.R
R/CDSeq.R
R/CPM.R
R/CibersortX.R
R/DWLS.R
R/MOMF.R
R/MuSiC.R
R/SCDC.R
R/Scaden.R
R/bisque.R
R/config.R
R/data.R
R/data_processing.R
R/deconvolution_algorithms.R
R/helper.R
R/visualisation.R
R/zzz.R
README.md
_pkgdown.yml
codecov.yml
data/RefData.RData
data/batch_ids_1.RData
data/batch_ids_2.RData
data/batch_ids_3.RData
data/bulk.RData
data/cell_type_annotations_1.RData
data/cell_type_annotations_2.RData
data/cell_type_annotations_3.RData
data/single_cell_data_1.RData
data/single_cell_data_2.RData
data/single_cell_data_3.RData
figure/unnamed-chunk-27-1.png
figure/unnamed-chunk-28-1.png
figure/unnamed-chunk-29-1.png
figure/unnamed-chunk-30-1.png
figure/unnamed-chunk-31-1.png
inst/small_test_data/batch_ids_small.txt
inst/small_test_data/bulk_small.csv
inst/small_test_data/cell_annotations_small.txt
inst/small_test_data/marker_genes_small.txt
inst/small_test_data/sc_object_small.csv
inst/test_models/bisque_model_small.csv
inst/test_models/bseq_model_small.csv
inst/test_models/bseqsc_model_small.csv
inst/test_models/cibersortx_model_small.tsv
inst/test_models/dwls_model_small.csv
inst/test_models/momf_model_small.csv
inst/test_results/autogenes_result_small.csv
inst/test_results/autogenes_result_small_new.csv
inst/test_results/bayesprism_result_small.csv
inst/test_results/bisque_result_small.csv
inst/test_results/cibersortx_result_small.tsv
inst/test_results/dwls_dwls_result_small.csv
inst/test_results/dwls_ols_result_small.csv
inst/test_results/dwls_svr_result_small.csv
inst/test_results/momf_result_small.csv
inst/test_results/music_result_small.csv
inst/test_results/scdc_result_ensemble.csv
inst/test_results/scdc_result_small.csv
man/RefData.Rd
man/anndata_checkload.Rd
man/anndata_is_identical.Rd
man/anndata_to_singlecellexperiment.Rd
man/autogenes_checkload.Rd
man/batch_ids_1.Rd
man/batch_ids_2.Rd
man/batch_ids_3.Rd
man/bseqsc_config.Rd
man/build_anndata.Rd
man/build_model.Rd
man/build_model_autogenes.Rd
man/build_model_bayesprism.Rd
man/build_model_bisque.Rd
man/build_model_bseqsc.Rd
man/build_model_cdseq.Rd
man/build_model_cibersortx.Rd
man/build_model_cpm.Rd
man/build_model_dwls.Rd
man/build_model_momf.Rd
man/build_model_music.Rd
man/build_model_scaden.Rd
man/build_model_scdc.Rd
man/bulk.Rd
man/calc_condition_number.Rd
man/calculate_cell_embedding.Rd
man/cell_type_annotations_1.Rd
man/cell_type_annotations_2.Rd
man/cell_type_annotations_3.Rd
man/check_and_install.Rd
man/check_container.Rd
man/check_credentials.Rd
man/convert_to_matrix.Rd
man/create_container_command.Rd
man/deconvolute.Rd
man/deconvolute_autogenes.Rd
man/deconvolute_bayesprism.Rd
man/deconvolute_bisque.Rd
man/deconvolute_bseqsc.Rd
man/deconvolute_cdseq.Rd
man/deconvolute_cibersortx.Rd
man/deconvolute_cpm.Rd
man/deconvolute_dwls.Rd
man/deconvolute_momf.Rd
man/deconvolute_music.Rd
man/deconvolute_scaden.Rd
man/deconvolute_scdc.Rd
man/deconvolution_methods.Rd
man/deescape_special_chars.Rd
man/dot-bisque_patched_deconvolution.Rd
man/dot-bisque_patched_model.Rd
man/escape_special_chars.Rd
man/extract_signature_autogenes.Rd
man/figures/README-pressure-1.png
man/get_cell_fractions_options.Rd
man/get_method_options.Rd
man/get_signature_matrix_options.Rd
man/get_single_cell_expression_set.Rd
man/init_python.Rd
man/install_all_python.Rd
man/install_autogenes.Rd
man/install_scaden.Rd
man/make_barplot.Rd
man/make_benchmarking_scatterplot.Rd
man/matrix_to_singlecellexperiment.Rd
man/normalize_deconv_results.Rd
man/omnideconvstartup.Rd
man/plot_deconvolution.Rd
man/python_available.Rd
man/read_anndata.Rd
man/required_packages.Rd
man/save_as_h5ad.Rd
man/scaden_checkload.Rd
man/scaden_predict.Rd
man/scaden_process.Rd
man/scaden_simulate.Rd
man/scaden_simulate_example.Rd
man/scaden_train.Rd
man/sces_are_identical.Rd
man/set_cibersortx_credentials.Rd
man/set_python.Rd
man/setup_apptainer_container.Rd
man/single_cell_data_1.Rd
man/single_cell_data_2.Rd
man/single_cell_data_3.Rd
man/singlecellexperiment_to_anndata.Rd
man/singlecellexperiment_to_matrix.Rd
man/transform_and_save_bulk.Rd
man/transform_and_save_single_cell.Rd
man/verbose_wrapper.Rd
man/write_anndata.Rd
omnideconv.Rproj
tests/createTestData.Rmd
tests/createTestData.log
tests/createTestData.pdf
tests/testthat.R
tests/testthat/create_test_files.R
tests/testthat/small_test_data/batch_ids_small.txt
tests/testthat/small_test_data/bulk_small.csv
tests/testthat/small_test_data/cell_annotations_small.txt
tests/testthat/small_test_data/marker_genes_small.txt
tests/testthat/small_test_data/sc_object_small.csv
tests/testthat/test-a-python.R
tests/testthat/test-b-buildmodel.R
tests/testthat/test-c-deconvolution.R
tests/testthat/test-d-dataconversion.R
tests/testthat/test_models/bisque_model_small.csv
tests/testthat/test_models/bseq_model_small.csv
tests/testthat/test_models/bseqsc_model_small.csv
tests/testthat/test_models/cibersortx_model_small.tsv
tests/testthat/test_models/dwls_model_small.csv
tests/testthat/test_models/momf_model_small.csv
tests/testthat/test_results/autogenes_result_small.csv
tests/testthat/test_results/autogenes_result_small_new.csv
tests/testthat/test_results/bayesprism_result_small.csv
tests/testthat/test_results/bisque_result_small.csv
tests/testthat/test_results/cibersortx_result_small.tsv
tests/testthat/test_results/dwls_dwls_result_small.csv
tests/testthat/test_results/dwls_ols_result_small.csv
tests/testthat/test_results/dwls_svr_result_small.csv
tests/testthat/test_results/momf_result_small.csv
tests/testthat/test_results/music_result_small.csv
tests/testthat/test_results/scdc_result_ensemble.csv
tests/testthat/test_results/scdc_result_small.csv
vignettes/.gitignore
vignettes/.old_vignette/images/bisque_matrices.png
vignettes/.old_vignette/images/bisque_prop.png
vignettes/.old_vignette/images/ciber_matrices.png
vignettes/.old_vignette/images/cibersortx_prop.png
vignettes/.old_vignette/images/dwls_matrices.png
vignettes/.old_vignette/images/dwls_prop.png
vignettes/.old_vignette/images/interchangeMatrix.png
vignettes/.old_vignette/images/introduction.jpg
vignettes/.old_vignette/images/logo.JPG
vignettes/.old_vignette/images/methods_table.png
vignettes/.old_vignette/images/momf_matrices.png
vignettes/.old_vignette/images/momf_prop.png
vignettes/.old_vignette/images/predictionVsGroundtruth.png
vignettes/.old_vignette/images/predictionVsGroundtruth_unnormalized.png
vignettes/.old_vignette/images/predictionVsGroundtruth_unnormalized_firstGeneration.png
vignettes/.old_vignette/images/propgrid_counts.png
vignettes/.old_vignette/images/propgrid_firstGeneration_counts.png
vignettes/.old_vignette/images/propgrid_firstGeneration_tpm.png
vignettes/.old_vignette/images/propgrid_mix.png
vignettes/.old_vignette/images/propgrid_tpm.png
vignettes/.old_vignette/images/scaden_prop.png
vignettes/.old_vignette/omnideconv_vignette.Rmd
vignettes/.old_vignette/references.bib
vignettes/.other_files/omnideconv_tumor_example.Rmd
vignettes/.other_files/vignette_example_tumor_data.Rmd
vignettes/logo/omnideconv_icon.jpg
vignettes/logo/omnideconv_icon.odg
vignettes/logo/omnideconv_icon.svg
vignettes/logo/omnideconv_logo.jpg
vignettes/logo/omnideconv_logo.odg
vignettes/logo/omnideconv_logo.svg
vignettes/notebook.html
vignettes/omnideconv_example.Rmd
vignettes/references.bib
vignettes/vignette_files/deconovlution.results.dwls.minor.rds
vignettes/vignette_files/deconvolution.dwls.rds
vignettes/vignette_files/deconvolution.results.bayesprism.rds
vignettes/vignette_files/signature.dwls.minor.rds
vignettes/vignette_files/signature.dwls.rds
