Files in snikumbh/seqArchR
Identify Different Architectures of Sequence Elements
.Rbuildignore
.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/make_sinuc_PWMs.R
R/plot_arch_for_clusters.R
R/plot_ggheatmap.R
R/prepare_data_from_FASTA.R
R/seqArchR.R
R/seqArchR_assertions.R
R/seqArchR_auxiliary_functionsI.R
R/seqArchR_auxiliary_functionsII.R
R/seqArchR_main.R
R/viz_basis_vectors.R
R/viz_matrix_of_acgt_image.R
R/zzz.R
README.md
_pkgdown.yml
codecov.yml
index.md
inst/CITATION
inst/extdata/example_data.fa.gz
inst/extdata/example_seqArchRresult.rds
inst/extdata/tssSeqsRaw.rds
inst/extdata/tssSinuc.rds
inst/python/perform_nmf.py
man/collate_clusters.Rd
man/collate_seqArchR_result.Rd
man/figures/seqArchR_algorithm_1080p_cropped.gif
man/figures/seqArchR_algorithm_static_illustrator_cropped.png
man/get_clBasVec.Rd
man/get_one_hot_encoded_seqs.Rd
man/get_seqs_clust_list.Rd
man/make_PWMs.Rd
man/plot_arch_for_clusters.Rd
man/plot_ggseqlogo_of_seqs.Rd
man/prepare_data_from_FASTA.Rd
man/seqArchR.Rd
man/seqs_str.Rd
man/set_config.Rd
man/viz_bas_vec.Rd
man/viz_pwm.Rd
man/viz_seqs_acgt_mat.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/figs/test-plotting-architectures-helper-functions/plot-arch-for-clusters-example.svg
tests/testthat.R
tests/testthat/seqArchRresult_checkpoint1.rds
tests/testthat/seqArchRresult_cv_check_timeFalse.rds
tests/testthat/seqArchRresult_stability_check_debugTrue.rds
tests/testthat/seqArchRresult_stability_check_timeFalse.rds
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_seqArchR_main.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/seqArchR-result-example-data.png
vignettes/seqArchR.Rmd
vignettes/seqArchR_algorithm_1080p_cropped.gif
vignettes/seqArchR_algorithm_static_illustrator_cropped.png
