Files in CompEpigen/scMethrix

Fast and efficient summarization of single cell whole genome bisulfate data

.github/.gitignore

.github/workflows/pkgdown.yaml

.gitignore

DESCRIPTION

LICENSE.md

NAMESPACE

NEWS.md R/accessory_funcs.R R/coord_ops.R R/read_beds.R R/scMethrix_clustering.R R/scMethrix_data.R R/scMethrix_dimensionality.R R/scMethrix_export.R R/scMethrix_plot.R R/scMethrix_transforms.R R/scmethrix_object.R R/scmethrix_operations.R R/validate_inputs.R R/zzz.R README.md

Rust/Rust_import_benchmark.xlsx

Rust/triplet_matrix/src/main.rs

Rust/triplet_matrix/src/triplet_matrix.rs

Rust/triplet_matrix/triplet_matrix.h5

_pkgdown.yml

benchmark/benchmark.R benchmark/profiling.R

data/scMethrix_data.rda

data_gen/data_gen.R

docs/404.html

docs/LICENSE.html

docs/articles/01_load_data.html

docs/articles/01_load_data_files/header-attrs-2.10/header-attrs.js

docs/articles/02_qc.html

docs/articles/02_qc_files/header-attrs-2.10/header-attrs.js

docs/articles/03_transforms.html

docs/articles/03_transforms_files/header-attrs-2.10/header-attrs.js

docs/articles/04_clustering.html

docs/articles/04_clustering_files/header-attrs-2.10/header-attrs.js

docs/articles/05_hdf5.html

docs/articles/05_hdf5_files/header-attrs-2.10/header-attrs.js

docs/articles/README.html

docs/articles/README_files/header-attrs-2.10/header-attrs.js

docs/articles/clustering.html

docs/articles/clustering_files/header-attrs-2.10/header-attrs.js

docs/articles/hdf5.html

docs/articles/hdf5_files/header-attrs-2.10/header-attrs.js

docs/articles/index.html

docs/articles/index_files/header-attrs-2.10/header-attrs.js

docs/articles/load_data.html

docs/articles/load_data_files/header-attrs-2.10/header-attrs.js

docs/articles/package_summary.PNG

docs/articles/qc.html

docs/articles/qc_files/header-attrs-2.10/header-attrs.js

docs/articles/scMethrix.html

docs/articles/scMethrix_files/header-attrs-2.10/header-attrs.js

docs/articles/transforms.html

docs/articles/transforms_files/header-attrs-2.10/header-attrs.js

docs/articles/x01_load_data.html

docs/articles/x01_load_data_files/header-attrs-2.10/header-attrs.js

docs/articles/x02_qc.html

docs/articles/x02_qc_files/header-attrs-2.10/header-attrs.js

docs/articles/x03_transforms.html

docs/articles/x03_transforms_files/header-attrs-2.10/header-attrs.js

docs/articles/x04_clustering.html

docs/articles/x04_clustering_files/header-attrs-2.10/header-attrs.js

docs/articles/x05_hdf5.html

docs/articles/x05_hdf5_files/header-attrs-2.10/header-attrs.js

docs/articles/x06_exporting.html

docs/articles/x06_exporting_files/header-attrs-2.10/header-attrs.js

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/append_colData.html

docs/reference/benchmark_imputation-1.png

docs/reference/benchmark_imputation.html

docs/reference/bin_granges.html

docs/reference/bin_scMethrix.html

docs/reference/binarize.html

docs/reference/binarize2.html

docs/reference/cast_granges.html

docs/reference/cluster_scMethrix.html

docs/reference/colbind.html

docs/reference/convert_HDF5_scMethrix.html

docs/reference/convert_scMethrix.html

docs/reference/convert_to_methrix.html

docs/reference/coverage_filter.html

docs/reference/dim_red_scMethrix.html

docs/reference/export_bed.html

docs/reference/generate_random_subset.html

docs/reference/generate_training_set.html

docs/reference/generic_scMethrix_function.html

docs/reference/get_distance_matrix.html

docs/reference/get_matrix.html

docs/reference/get_metadata_stats.html

docs/reference/get_palette.html

docs/reference/get_region_summary.html

docs/reference/get_sample_name.html

docs/reference/get_shape.html

docs/reference/get_source_idx.html

docs/reference/get_stats.html

docs/reference/has_cov.html

docs/reference/impute_by_RF.html

docs/reference/impute_by_iPCA.html

docs/reference/impute_by_kNN.html

docs/reference/impute_by_melissa.html

docs/reference/impute_regions.html

docs/reference/impute_scMethrix.html

docs/reference/index.html

docs/reference/is_h5.html

docs/reference/load_HDF5_scMethrix.html

docs/reference/mask_by_coverage.html

docs/reference/mask_by_sample.html

docs/reference/mask_by_variance.html

docs/reference/mask_helper.html

docs/reference/mask_non_variable.html

docs/reference/mask_scMethrix.html

docs/reference/merge_scMethrix.html

docs/reference/order_by_sd.html

docs/reference/parse_source_idx.html

docs/reference/pca_scMethrix.html

docs/reference/plot_coverage-1.png

docs/reference/plot_coverage.html

docs/reference/plot_density-1.png

docs/reference/plot_density.html

docs/reference/plot_dim_red-1.png

docs/reference/plot_dim_red.html

docs/reference/plot_pca-1.png

docs/reference/plot_pca.html

docs/reference/plot_sparsity-1.png

docs/reference/plot_sparsity.html

docs/reference/plot_stats-1.png

docs/reference/plot_stats.html

docs/reference/plot_tsne.html

docs/reference/plot_umap.html

docs/reference/plot_violin-1.png

docs/reference/plot_violin.html

docs/reference/prepare_plot_data.html

docs/reference/read_bed_by_index.html

docs/reference/read_beds.html

docs/reference/read_hdf5_data.html

docs/reference/read_index.html

docs/reference/read_mem_data.html

docs/reference/reduce_cpgs.html

docs/reference/reduce_matrix.html

docs/reference/remove_assay.html

docs/reference/remove_uncovered.html

docs/reference/save_HDF5_scMethrix.html

docs/reference/scMethrix-class.html

docs/reference/scMethrix_data.html

docs/reference/scMethrix_theme.html

docs/reference/split_granges.html

docs/reference/split_time.html

docs/reference/split_vector.html

docs/reference/start_time.html

docs/reference/stop_time.html

docs/reference/subset_ref_cpgs.html

docs/reference/subset_scMethrix.html

docs/reference/transform_assay.html

docs/reference/tsne_scMethrix.html

docs/reference/umap_scMethrix.html

inst/extdata/C1.bedgraph

inst/extdata/C2.bedgraph

inst/extdata/C3.bedgraph

inst/extdata/C4.bedgraph

man/append_colData.Rd man/benchmark_imputation.Rd man/bin_granges.Rd man/bin_scMethrix.Rd man/binarize.Rd man/cast_datatable.Rd man/cast_granges.Rd man/cluster_scMethrix.Rd man/colbind.Rd man/collapse_samples.Rd man/convert_HDF5_scMethrix.Rd man/convert_scMethrix.Rd man/dim_red_scMethrix.Rd man/dot-validateArg.Rd man/dot-validateAssay.Rd man/dot-validateExp.Rd man/dot-validateThreads.Rd man/dot-validateValue.Rd man/export_beds.Rd man/export_bigwigs.Rd man/export_bsseq.Rd man/export_methrix.Rd man/extract_CpGs.Rd man/fill.Rd man/generate_random_subset.Rd man/generate_training_set.Rd man/generic_scMethrix_function.Rd man/get_distance_matrix.Rd man/get_matrix.Rd man/get_metadata_stats.Rd man/get_palette.Rd man/get_region_summary.Rd man/get_sample_name.Rd man/get_shape.Rd man/get_source_idx.Rd man/get_stats.Rd man/has_cov.Rd man/impute_by_melissa.Rd man/impute_regions.Rd man/is_h5.Rd man/liftover_CpGs.Rd man/load_HDF5_scMethrix.Rd man/mask_by_coverage.Rd man/mask_by_sample.Rd man/mask_by_variance.Rd man/mask_helper.Rd man/merge_scMethrix.Rd man/parse_source_idx.Rd man/plot_coverage.Rd man/plot_density.Rd man/plot_dim_red.Rd man/plot_sparsity.Rd man/plot_stats.Rd man/plot_violin.Rd man/prepare_plot_data.Rd man/read_bed_by_index.Rd man/read_beds.Rd man/read_hdf5_data.Rd man/read_index.Rd man/read_mem_data.Rd man/reduce_cpgs.Rd man/remove_assay.Rd man/remove_uncovered.Rd man/save_HDF5_scMethrix.Rd man/scMethrix-class.Rd man/scMethrix_data.Rd man/scMethrix_theme.Rd man/split_time.Rd man/split_vector.Rd man/start_time.Rd man/stop_time.Rd man/subset_ref_cpgs.Rd man/subset_scMethrix.Rd man/transform_assay.Rd sandbox/R_import_benchmark.R

sandbox/R_import_benchmark.xlsx

sandbox/annotation.R sandbox/bedtools_import.R sandbox/cell_colData.R sandbox/direct_import.R sandbox/generate_bedgraphs.R sandbox/generic_setup_stuff.R sandbox/genomicranges_import.R sandbox/methrix_compare.R sandbox/misc_functions.R sandbox/rust_import.R sandbox/summarized_exp.R sandbox/utility_test_functions.R

scMethrix.Rproj

tests/testobj.R tests/testthat.R tests/testthat/Rplots.pdf tests/testthat/setup.R tests/testthat/test-accessory_funcs.R tests/testthat/test-read_beds.R tests/testthat/test-scMethrix-test.R tests/testthat/test-scMethrix_clustering.R tests/testthat/test-scMethrix_dimensionality.R tests/testthat/test-scMethrix_object.R tests/testthat/test-scMethrix_operations.R tests/testthat/test-scMethrix_plot.R tests/testthat/test-scMethrix_transforms.R

vignettes/package_summary.PNG

vignettes/x01_load_data.Rmd vignettes/x02_qc.Rmd vignettes/x03_transforms.Rmd vignettes/x04_clustering.Rmd vignettes/x05_hdf5.Rmd vignettes/x06_exporting.Rmd

CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.