Files in ggDNAvis
'ggplot2'-Based Tools for Visualising DNA Sequences and Modifications
MD5
NEWS.md
NAMESPACE
DESCRIPTION
LICENSE
R/dna_tools.R
R/visualise_many_sequences.R
R/visualise_single_sequence.R
R/merge_with_metadata.R
R/ggDNAvis-package.R
R/parse_methylation_from_fastq.R
R/visualise_methylation.R
inst/extdata/example_many_sequences_raw.fastq
inst/extdata/example_many_sequences_raw_modified.fastq
inst/extdata/example_many_sequences_metadata.csv
tests/testthat.R
tests/testthat/test-visualise_methylation.R
tests/testthat/test-visualise_many_sequences.R
tests/testthat/test-merge_with_metadata.R
tests/testthat/test-dna_tools.R
tests/testthat/test-visualise_single_sequence.R
tests/testthat/test-parse_methylation_from_fastq.R
tests/testthat/reference_output_data/example_many_sequences_no_quality.fastq
tests/testthat/reference_output_data/example_many_sequences_unmodified.fastq
tests/testthat/reference_output_data/example_many_sequences_altered_modification.fastq
tests/testthat/reference_output_data/example_many_sequences.fastq
tests/testthat/reference_output_data/example_many_sequences_unmodified_no_quality.fastq
tests/testthat/reference_output_data/example_many_sequences_directional.fastq
tests/testthat/reference_output_data/example_many_sequences_c+m_no_question.fastq
tests/testthat/reference_output_data/example_many_sequences_unmodified_directional.fastq
tests/testthat/reference_output_data/example_many_sequences_metadata.csv
tests/testthat/reference_output_data/example_many_sequences_altered_with_blank_tags.fastq
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_10.jpg
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_05.png
tests/testthat/test_plot_images/visualise_methylation_test_06.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_18.png
tests/testthat/test_plot_images/visualise_many_sequences_test_10.png
tests/testthat/test_plot_images/visualise_many_sequences_test_05.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_24.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_17.png
tests/testthat/test_plot_images/visualise_many_sequences_test_06.png
tests/testthat/test_plot_images/visualise_methylation_test_04.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_02.png
tests/testthat/test_plot_images/visualise_methylation_test_08.png
tests/testthat/test_plot_images/keep.txt
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_06.png
tests/testthat/test_plot_images/visualise_methylation_scalebar_test_04.png
tests/testthat/test_plot_images/visualise_methylation_test_03.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_23.png
tests/testthat/test_plot_images/visualise_many_sequences_test_09.png
tests/testthat/test_plot_images/visualise_many_sequences_test_02.png
tests/testthat/test_plot_images/visualise_many_sequences_test_12.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_01.png
tests/testthat/test_plot_images/visualise_methylation_test_01.png
tests/testthat/test_plot_images/visualise_many_sequences_test_15.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_03.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_12.PNG
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_25.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_07.pNg
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_08.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_22.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_28.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_11.PNG
tests/testthat/test_plot_images/visualise_many_sequences_test_01.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_15.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_26.png
tests/testthat/test_plot_images/visualise_methylation_test_05.png
tests/testthat/test_plot_images/visualise_many_sequences_test_08.png
tests/testthat/test_plot_images/visualise_methylation_scalebar_test_05.png
tests/testthat/test_plot_images/visualise_many_sequences_test_14.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_13.PNG
tests/testthat/test_plot_images/visualise_methylation_test_02.png
tests/testthat/test_plot_images/visualise_methylation_test_07.png
tests/testthat/test_plot_images/visualise_many_sequences_test_04.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_04.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_27.png
tests/testthat/test_plot_images/visualise_many_sequences_test_03.png
tests/testthat/test_plot_images/visualise_methylation_scalebar_test_03.png
tests/testthat/test_plot_images/visualise_many_sequences_test_07.png
tests/testthat/test_plot_images/visualise_many_sequences_test_11.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_29.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_19.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_09.jpg
tests/testthat/test_plot_images/visualise_many_sequences_test_13.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_20.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_16.png
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_14.PNG
tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_21.png
tests/testthat/test_output_data/example_many_sequences_no_quality.fastq
tests/testthat/test_output_data/example_many_sequences_unmodified.fastq
tests/testthat/test_output_data/example_many_sequences_altered_modification.fastq
tests/testthat/test_output_data/keep.txt
tests/testthat/test_output_data/example_many_sequences.fastq
tests/testthat/test_output_data/example_many_sequences_unmodified_no_quality.fastq
tests/testthat/test_output_data/example_many_sequences_directional.fastq
tests/testthat/test_output_data/example_many_sequences_c+m_no_question.fastq
tests/testthat/test_output_data/example_many_sequences_unmodified_directional.fastq
tests/testthat/test_output_data/example_many_sequences_altered_with_blank_tags.fastq
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_10.jpg
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_05.png
tests/testthat/reference_images/visualise_methylation_test_06.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_18.png
tests/testthat/reference_images/visualise_many_sequences_test_10.png
tests/testthat/reference_images/visualise_many_sequences_test_05.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_24.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_17.png
tests/testthat/reference_images/visualise_many_sequences_test_06.png
tests/testthat/reference_images/visualise_methylation_test_04.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_02.png
tests/testthat/reference_images/visualise_methylation_test_08.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_06.png
tests/testthat/reference_images/visualise_methylation_scalebar_test_04.png
tests/testthat/reference_images/visualise_methylation_test_03.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_23.png
tests/testthat/reference_images/visualise_many_sequences_test_09.png
tests/testthat/reference_images/visualise_many_sequences_test_02.png
tests/testthat/reference_images/visualise_many_sequences_test_12.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_01.png
tests/testthat/reference_images/visualise_methylation_test_01.png
tests/testthat/reference_images/visualise_many_sequences_test_15.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_03.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_12.PNG
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_25.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_07.pNg
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_08.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_22.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_28.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_11.PNG
tests/testthat/reference_images/visualise_many_sequences_test_01.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_15.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_26.png
tests/testthat/reference_images/visualise_methylation_test_05.png
tests/testthat/reference_images/visualise_many_sequences_test_08.png
tests/testthat/reference_images/visualise_methylation_scalebar_test_05.png
tests/testthat/reference_images/visualise_many_sequences_test_14.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_13.PNG
tests/testthat/reference_images/visualise_methylation_test_02.png
tests/testthat/reference_images/visualise_methylation_test_07.png
tests/testthat/reference_images/visualise_many_sequences_test_04.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_04.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_27.png
tests/testthat/reference_images/visualise_many_sequences_test_03.png
tests/testthat/reference_images/visualise_methylation_scalebar_test_03.png
tests/testthat/reference_images/visualise_many_sequences_test_07.png
tests/testthat/reference_images/visualise_many_sequences_test_11.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_29.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_19.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_09.jpg
tests/testthat/reference_images/visualise_many_sequences_test_13.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_20.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_16.png
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_14.PNG
tests/testthat/reference_images/sone_2019_f1_1_expanded_test_21.png
data/sequence_colour_palettes.rda
data/example_many_sequences.rda
data/fastq_quality_scores.rda
man/convert_modification_to_number_vector.Rd
man/visualise_many_sequences.Rd
man/extract_and_sort_sequences.Rd
man/debug_join_vector_str.Rd
man/write_modified_fastq.Rd
man/create_image_data.Rd
man/reverse_complement.Rd
man/convert_sequences_to_annotations.Rd
man/convert_MM_vector_to_locations.Rd
man/write_fastq.Rd
man/convert_input_seq_to_sequence_list.Rd
man/example_many_sequences.Rd
man/sequence_colour_palettes.Rd
man/visualise_single_sequence.Rd
man/convert_sequence_to_numbers.Rd
man/reverse_sequence_if_needed.Rd
man/merge_fastq_with_metadata.Rd
man/reverse_probabilities_if_needed.Rd
man/string_to_vector.Rd
man/visualise_methylation.Rd
man/visualise_methylation_colour_scale.Rd
man/vector_to_string.Rd
man/fastq_quality_scores.Rd
man/merge_methylation_with_metadata.Rd
man/rasterise_matrix.Rd
man/ggDNAvis-package.Rd
man/read_fastq.Rd
man/extract_methylation_from_dataframe.Rd
man/reverse_locations_if_needed.Rd
man/convert_locations_to_MM_vector.Rd
man/reverse_quality_if_needed.Rd
man/convert_base_to_number.Rd
man/debug_join_vector_num.Rd
man/read_modified_fastq.Rd
man/figures/logo.png
man/figures/many_sequences_for_sticker.svg
man/figures/ggDNAvis.png
man/figures/ggDNAvis_sticker.R
