Files in GenomeNet/deepG
Deep Learning for Genome Sequence Data
.Rbuildignore
.github/workflows/check.yml
.github/workflows/pkgdown.yaml
.github/workflows/rhub.yaml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/callbacks.R
R/create_model_genomenet.R
R/create_model_lstm_cnn.R
R/create_model_set_learning.R
R/create_model_transformer.R
R/create_model_twin_network.R
R/create_model_utils.R
R/custom_layers.R
R/data.R
R/evaluation.R
R/generator_csv.R
R/generator_folder.R
R/generator_folder_collect.R
R/generator_lm.R
R/generator_random.R
R/generator_rds.R
R/generator_utils.R
R/generators.R
R/globals.R
R/help_functions.R
R/metrics.R
R/n_gram.R
R/package.R
R/predict.R
R/preprocess.R
R/train.R
R/train_cpc.R
R/utils-pipe.R
R/visualization.R
R/write_dummy_data.R
README.Rmd
README.md
_pkgdown.yml
data-raw/crispr_1000.txt
data-raw/crispr_sample.R
data-raw/crispr_sample.txt
data-raw/ecoli.fasta
data-raw/ecoli_small.R
data-raw/ecoli_small.fasta
data-raw/parenthesis.R
data-raw/parenthesis.txt
data/crispr_sample.rda
data/ecoli_small.rda
data/parenthesis.rda
docs/.nojekyll
docs/404.html
docs/CNAME
docs/LICENSE-text.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/data_generator.html
docs/articles/getting_started.html
docs/articles/getting_started_files/figure-html/unnamed-chunk-10-1.png
docs/articles/getting_started_files/figure-html/unnamed-chunk-7-1.png
docs/articles/index.html
docs/articles/integrated_gradient.html
docs/articles/integrated_gradient_files/figure-html/unnamed-chunk-12-1.png
docs/articles/integrated_gradient_files/figure-html/unnamed-chunk-13-1.png
docs/articles/integrated_gradient_files/figure-html/unnamed-chunk-5-1.png
docs/articles/integrated_gradient_files/figure-html/unnamed-chunk-9-1.png
docs/articles/tb_images/acc.png
docs/articles/tb_images/auc.png
docs/articles/tb_images/bal_acc.png
docs/articles/tb_images/cm_train.png
docs/articles/tb_images/cm_val.png
docs/articles/tb_images/f1.png
docs/articles/tb_images/files_seen.png
docs/articles/tb_images/hparam.png
docs/articles/tb_images/loss.png
docs/articles/tb_images/lr.png
docs/articles/training_types.html
docs/articles/training_types_files/figure-html/unnamed-chunk-12-1.png
docs/articles/training_types_files/figure-html/unnamed-chunk-20-1.png
docs/articles/training_types_files/figure-html/unnamed-chunk-23-1.png
docs/articles/training_types_files/figure-html/unnamed-chunk-7-1.png
docs/articles/training_types_files/figure-html/unnamed-chunk-9-1.png
docs/articles/using_tb.html
docs/articles/using_tb_files/figure-html/unnamed-chunk-9-1.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/sitemap.xml
docs/tutorial_html/data_generator.html
docs/tutorial_html/getting_started.html
docs/tutorial_html/getting_started_files/figure-html/unnamed-chunk-10-1.png
docs/tutorial_html/getting_started_files/figure-html/unnamed-chunk-7-1.png
docs/tutorial_html/index.html
docs/tutorial_html/integrated_gradient.html
docs/tutorial_html/integrated_gradient_files/figure-html/unnamed-chunk-12-1.png
docs/tutorial_html/integrated_gradient_files/figure-html/unnamed-chunk-13-1.png
docs/tutorial_html/integrated_gradient_files/figure-html/unnamed-chunk-5-1.png
docs/tutorial_html/integrated_gradient_files/figure-html/unnamed-chunk-9-1.png
docs/tutorial_html/tb_images/acc.png
docs/tutorial_html/tb_images/auc.png
docs/tutorial_html/tb_images/bal_acc.png
docs/tutorial_html/tb_images/cm_train.png
docs/tutorial_html/tb_images/cm_val.png
docs/tutorial_html/tb_images/f1.png
docs/tutorial_html/tb_images/files_seen.png
docs/tutorial_html/tb_images/hparam.png
docs/tutorial_html/tb_images/loss.png
docs/tutorial_html/tb_images/lr.png
docs/tutorial_html/training_types.html
docs/tutorial_html/training_types_files/figure-html/unnamed-chunk-12-1.png
docs/tutorial_html/training_types_files/figure-html/unnamed-chunk-20-1.png
docs/tutorial_html/training_types_files/figure-html/unnamed-chunk-23-1.png
docs/tutorial_html/training_types_files/figure-html/unnamed-chunk-7-1.png
docs/tutorial_html/training_types_files/figure-html/unnamed-chunk-9-1.png
docs/tutorial_html/using_tb.html
docs/tutorial_html/using_tb_files/figure-html/unnamed-chunk-9-1.png
man/auc_wrapper.Rd
man/balanced_acc_wrapper.Rd
man/compile_model.Rd
man/conf_matrix_cb.Rd
man/create_dummy_data.Rd
man/create_model_genomenet.Rd
man/create_model_lstm_cnn.Rd
man/create_model_lstm_cnn_multi_input.Rd
man/create_model_lstm_cnn_target_middle.Rd
man/create_model_lstm_cnn_time_dist.Rd
man/create_model_transformer.Rd
man/create_model_twin_network.Rd
man/crispr_sample.Rd
man/dataset_from_gen.Rd
man/deepG-package.Rd
man/early_stopping_time_cb.Rd
man/ecoli_small.Rd
man/evaluate_linear.Rd
man/evaluate_model.Rd
man/evaluate_sigmoid.Rd
man/evaluate_softmax.Rd
man/exp_decay.Rd
man/f1_wrapper.Rd
man/figures/aws.png
man/figures/bmbf.jpeg
man/figures/dfg.jpg
man/figures/figure.png
man/figures/hzi.jpg
man/figures/logo.png
man/figures/logo2.png
man/figures/logo_deepg.svg
man/figures/logo_small.png
man/figures/unnamed-chunk-8-1.png
man/focal_loss_multiclass.Rd
man/generator_dummy.Rd
man/generator_fasta_label_folder.Rd
man/generator_fasta_label_folder_wrapper.Rd
man/generator_fasta_label_header_csv.Rd
man/generator_fasta_lm.Rd
man/generator_initialize.Rd
man/generator_random.Rd
man/generator_rds.Rd
man/get_class_weight.Rd
man/get_generator.Rd
man/get_output_activations.Rd
man/get_start_ind.Rd
man/heatmaps_integrated_grad.Rd
man/int_to_n_gram.Rd
man/integrated_gradients.Rd
man/layer_aggregate_time_dist_wrapper.Rd
man/layer_pos_embedding_wrapper.Rd
man/layer_pos_sinusoid_wrapper.Rd
man/layer_transformer_block_wrapper.Rd
man/load_cp.Rd
man/load_prediction.Rd
man/loss_cl.Rd
man/merge_models.Rd
man/model_card_cb.Rd
man/n_gram_dist.Rd
man/n_gram_of_matrix.Rd
man/noisy_loss_wrapper.Rd
man/one_hot_to_seq.Rd
man/parenthesis.Rd
man/pipe.Rd
man/plot_cm.Rd
man/plot_roc.Rd
man/predict_model.Rd
man/predict_with_n_gram.Rd
man/remove_add_layers.Rd
man/remove_checkpoints.Rd
man/reset_states_cb.Rd
man/reshape_input.Rd
man/reshape_tensor.Rd
man/resume_training_from_model_card.Rd
man/seq_encoding_label.Rd
man/seq_encoding_lm.Rd
man/sgdr.Rd
man/split_fasta.Rd
man/stepdecay.Rd
man/summarize_states.Rd
man/train_model.Rd
man/train_model_cpc.Rd
man/validation_after_training_cb.Rd
tests/testthat.R
tests/testthat/a.fastq
tests/testthat/add_seq.csv
tests/testthat/coverage_data/x/a.fasta
tests/testthat/coverage_data/x/b.fasta
tests/testthat/coverage_data/y/a.fasta
tests/testthat/coverage_data/y/b.fasta
tests/testthat/example_model_cpu_new_full_model.hdf5
tests/testthat/fasta/x.fasta
tests/testthat/fasta/y.fasta
tests/testthat/fasta_2/a.fasta
tests/testthat/fasta_2/b.fasta
tests/testthat/fasta_3/a.fasta
tests/testthat/fasta_3/b.fasta
tests/testthat/fastq/a.fastq
tests/testthat/fastq/b.fastq
tests/testthat/fastq/c.fastq
tests/testthat/label.csv
tests/testthat/label_folder/x/x1.fasta
tests/testthat/label_folder/x/x2.fasta
tests/testthat/label_folder/y/y1.fasta
tests/testthat/label_folder/y/y2.fasta
tests/testthat/label_folder/z/z1.fasta
tests/testthat/label_folder/z/z2.fasta
tests/testthat/n_gram_rds/z.rds
tests/testthat/output_label.csv
tests/testthat/rds/z1.rds
tests/testthat/rds/z2.rds
tests/testthat/rds_lm/z1.rds
tests/testthat/rds_lm/z2.rds
tests/testthat/read_data/a_R1.fastq
tests/testthat/read_data/a_R2.fastq
tests/testthat/read_data/b_R1.fastq
tests/testthat/read_data/b_R2.fastq
tests/testthat/read_data_2/label_a/a_R1.fastq
tests/testthat/read_data_2/label_a/a_R2.fastq
tests/testthat/read_data_2/label_a/b_R1.fastq
tests/testthat/read_data_2/label_a/b_R2.fastq
tests/testthat/read_data_2/label_b/a_R1.fastq
tests/testthat/read_data_2/label_b/a_R2.fastq
tests/testthat/read_data_2/label_b/b_R1.fastq
tests/testthat/read_data_2/label_b/b_R2.fastq
tests/testthat/test-generators.R
tests/testthat/test-gpuManagement.R
tests/testthat/test-predict.R
tests/testthat/test-preprocess.R
tests/testthat/test-tensorboard.R
tests/testthat/test-train.R
vignettes/data_generator.Rmd
vignettes/getting_started.Rmd
vignettes/integrated_gradient.Rmd
vignettes/tb_images/acc.png
vignettes/tb_images/auc.png
vignettes/tb_images/bal_acc.png
vignettes/tb_images/cm_train.png
vignettes/tb_images/cm_val.png
vignettes/tb_images/f1.png
vignettes/tb_images/files_seen.png
vignettes/tb_images/hparam.png
vignettes/tb_images/loss.png
vignettes/tb_images/lr.png
vignettes/train_1_dir/label_1_train_file_1.fasta
vignettes/train_2_dir/label_2_train_file_1.fasta
vignettes/training_types.Rmd
vignettes/using_tb.Rmd
vignettes/val_1_dir/label_1_train_file_1.fasta
vignettes/val_2_dir/label_2_train_file_1.fasta
