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
