Files in snikumbh/archR

Identify Different Architectures of Sequence Elements

.Rbuildignore

.covrignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.github/workflows/pkgdown.yaml

.github/workflows/test-coverage.yaml

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/NMF_model_selection_functions.R R/NMF_model_selection_functionsII.R R/archR.R R/archR_assertions.R R/archR_auxiliary_functionsI.R R/archR_auxiliary_functionsII.R R/archR_main.R R/make_sinuc_PWMs.R R/plot_arch_for_clusters.R R/plot_ggheatmap.R R/prepare_data_from_FASTA.R R/runArchRUI.R R/viz_basis_vectors.R R/viz_matrix_of_acgt_image.R R/zzz.R README.md

_pkgdown.yml

archR.Rproj

codecov.yml

index.md

inst/CITATION

inst/extdata/example_archRresult.rds

inst/extdata/example_data.fa

inst/python/perform_nmf.py

man/archR.Rd man/archR_set_config.Rd man/collate_archR_result.Rd man/collate_clusters.Rd

man/figures/archR_algorithm_1080p_cropped.gif

man/figures/archR_algorithm_static_illustrator_cropped.png

man/get_clBasVec.Rd man/get_one_hot_encoded_seqs.Rd man/get_seqs_clust_list.Rd man/handle_dir_creation.Rd man/make_dinuc_PWMs.Rd man/make_sinuc_PWMs.Rd man/plot_arch_for_clusters.Rd man/plot_ggheatmap.Rd man/plot_ggseqlogo.Rd man/plot_ggseqlogo_of_seqs.Rd man/prepare_data_from_FASTA.Rd man/run_archR_UI.Rd man/seqs_str.Rd man/viz_bas_vec_heatmap_seqlogo.Rd man/viz_seqs_acgt_mat_from_seqs.Rd

tests/figs/deps.txt

tests/figs/plotting-features-matrix-as-ggheatmap/ggheatmap-plot-example.svg

tests/figs/plotting-seqlogo-w-ggseqlogo/ggseqlogo-plot-example.svg

tests/figs/representing-sequences-as-an-image/sample-image-of-sequences.svg

tests/testthat.R tests/testthat/test_archR_main.R tests/testthat/test_auxiliary_functionsI.R tests/testthat/test_auxiliary_functionsII.R tests/testthat/test_fasta_file_exists.R tests/testthat/test_fasta_input.R tests/testthat/test_model_selection_functions.R tests/testthat/test_nmf_solving.R tests/testthat/test_one_hot_encoding_functions.R tests/testthat/test_plot_arch_for_clusters.R tests/testthat/test_plot_ggseqlogo.R tests/testthat/test_plot_heatmap.R tests/testthat/test_seqs_image_representation.R tests/testthat/test_viz_basis_vectors_heatmap.R tests/testthat/test_viz_basis_vectors_heatmap_seqlogo.R tests/testthat/test_viz_basis_vectors_seqlogo.R

vignettes/.gitignore

vignettes/archR-result-example-data.png

vignettes/archR.Rmd

vignettes/archR_algorithm_1080p_cropped.gif

vignettes/archR_algorithm_static_illustrator_cropped.png

snikumbh/archR documentation built on July 5, 2021, 8:46 a.m.