Files in satyausc/methylDNAshapeHTmethod
Reproduce all the plots used in the paper "methylDNAshape"

.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/CpG_containing_motifs_from_MotifDb.R R/DNaseI_bias_profiler.R R/a_tracts_mgw_profiler.R R/a_tracts_paired_t_test_calculator.R R/a_tracts_statistics_calculator.R R/assign_significance_labels.R R/common_observation_finder.R R/data_retriever.R R/feature_color_scheme.R R/feature_subset_selector.R R/figure1_generator.R R/figure2_generator.R R/figure3_generator.R R/figure4_generator.R R/globalParam.cfg.R R/motif_counts_plotter.R R/pentamer_data_from_QuerTable_getter.R R/plot_themes.R R/rcsb_statistics_plotter.R R/reverse_complement.R R/set_axis_limits.R R/shape_delta_plot_profiler.R R/shape_scatter_and_box_plot_generator.R R/shape_scatter_plot_profiler.R README.md
inst/extdata/DNaseI/all_hexamer_data/Allans_new_data_high_meth.SR
inst/extdata/DNaseI/all_hexamer_data/Allans_new_data_high_meth.shape
inst/extdata/DNaseI/all_hexamer_data/Allans_new_data_low_meth.SR
inst/extdata/DNaseI/all_hexamer_data/Allans_new_data_low_meth.shape
inst/extdata/DNaseI/all_hexamer_data/README.md
inst/extdata/DNaseI/all_hexamer_data/all_methylated_hexamers.2dG
inst/extdata/DNaseI/all_hexamer_data/all_methylated_hexamers.seq
inst/extdata/DNaseI/all_hexamer_data/all_methylated_hexamers.shape
inst/extdata/DNaseI/all_hexamer_data/all_methylated_hexamers_0_replaced_by_minimum_cutrate.2dG
inst/extdata/DNaseI/all_hexamer_data/all_unmethylated_hexamers.2dG
inst/extdata/DNaseI/all_hexamer_data/all_unmethylated_hexamers.seq
inst/extdata/DNaseI/all_hexamer_data/all_unmethylated_hexamers.shape
inst/extdata/DNaseI/all_hexamer_data/all_unmethylated_hexamers_0_replaced_by_minimum_cutrate.2dG
inst/extdata/DNaseI/all_hexamer_data/save_table.R
inst/extdata/DNaseI/all_hexamer_data/tier1_table
inst/extdata/DNaseI/all_hexamer_data/tier2_table
inst/extdata/DNaseI/all_hexamer_data/tier3_table
inst/extdata/DNaseI/all_hexamer_data/tier4_table
inst/extdata/DNaseI/all_hexamer_data/tier5_table
inst/extdata/DNaseI/all_hexamer_data/unmethylated_hexamer_data_with_new_CG_context_table.shape
inst/extdata/PDB_count_analyses/QueryPDBCounts.py
inst/extdata/PDB_count_analyses/README.md
inst/extdata/PDB_count_analyses/TF_containing_CpG.results
inst/extdata/PDB_count_analyses/count_data.results
inst/extdata/PDB_count_analyses/count_statistics_more_refined.results
inst/extdata/figure_config_yamls/DNaseI_3dG.yaml
inst/extdata/figure_config_yamls/barplot.yaml
inst/extdata/figure_config_yamls/delta_shape.yaml
inst/extdata/figure_config_yamls/delta_shape_plot_object.yaml
inst/extdata/figure_config_yamls/scatter_and_box.yaml
inst/extdata/figure_config_yamls/scatter_shape.yaml
inst/extdata/figure_config_yamls/scatter_shape_plot_object.yaml
inst/extdata/figure_config_yamls/up_and_down.yaml
inst/extdata/images_for_README/f1-dpi-300.png
inst/extdata/images_for_README/f1-dpi-300.tiff
inst/extdata/images_for_README/f2-dpi-300.png
inst/extdata/images_for_README/f2-dpi-300.tiff
inst/extdata/images_for_README/f3-dpi-300.png
inst/extdata/images_for_README/f3-dpi-300.tiff
inst/extdata/images_for_README/f4-dpi-300.png
inst/extdata/images_for_README/f4-dpi-300.tiff
inst/extdata/methyl-DNAshape_analyses/A_tracts_ends_with_MG_paired_T_test_pos7.dat
inst/extdata/methyl-DNAshape_analyses/A_tracts_ends_with_MG_paired_T_test_pos8.dat
inst/extdata/methyl-DNAshape_analyses/DNAshape_pentamers.MGW.raw.dat
inst/extdata/methyl-DNAshape_analyses/DNAshape_table_with_CG_context.dat
inst/extdata/methyl-DNAshape_analyses/QueryTable.DNAshape.dat
inst/extdata/methyl-DNAshape_analyses/QueryTable.methyl-DNAshape.dat
inst/extdata/methyl-DNAshape_analyses/QueryTable.methyl-DNAshape_with_M_and_g.dat
inst/extdata/methyl-DNAshape_analyses/delta_meth_vs_unmeth.sub
inst/extdata/methyl-DNAshape_analyses/effect_on_Atracts.avg
inst/extdata/methyl-DNAshape_analyses/effect_on_Atracts_another_format.avg
inst/extdata/methyl-DNAshape_analyses/meth_pentamers_with_MpG.avg
inst/extdata/methyl-DNAshape_analyses/meth_pentamers_with_MpG.avg.back
inst/extdata/methyl-DNAshape_analyses/meth_used.abs
inst/extdata/methyl-DNAshape_analyses/methyl-DNAshape_pentamers.MGW.raw.dat
inst/extdata/methyl-DNAshape_analyses/methylated_a_tract_with_CG_in_pentamer.seq
inst/extdata/methyl-DNAshape_analyses/methylated_a_tracts.raw
inst/extdata/methyl-DNAshape_analyses/methylated_a_tracts_ending_with_M.seq
inst/extdata/methyl-DNAshape_analyses/methylated_a_tracts_ending_with_M_pos7.raw.dat
inst/extdata/methyl-DNAshape_analyses/order_legend
inst/extdata/methyl-DNAshape_analyses/seethis.sub
inst/extdata/methyl-DNAshape_analyses/unmeth_in_meth_format_used.abs
inst/extdata/methyl-DNAshape_analyses/unmeth_pentamers_with_CpG.avg
inst/extdata/methyl-DNAshape_analyses/unmeth_pentamers_with_CpG.avg.back
inst/extdata/methyl-DNAshape_analyses/unmethylated.MGW.raw.dat
inst/extdata/methyl-DNAshape_analyses/unmethylated_a_tract_with_CG_in_pentamer.seq
inst/extdata/methyl-DNAshape_analyses/unmethylated_a_tracts.raw
inst/extdata/methyl-DNAshape_analyses/unmethylated_a_tracts_ending_with_C.seq
inst/extdata/methyl-DNAshape_analyses/unmethylated_a_tracts_ending_with_C_pos7.raw.dat
inst/python/feature_vector_generation/NNNCGN_missing_included.seq
inst/python/feature_vector_generation/NNNMGN_missing_included.seq
inst/python/feature_vector_generation/README.md
inst/python/feature_vector_generation/mvmvmv
inst/python/feature_vector_generation/src/autoconvert.py
inst/python/feature_vector_generation/src/autoconvert.pyc
inst/python/feature_vector_generation/src/build_feature_vector.py
inst/python/feature_vector_generation/src/build_feature_vector.pyc
inst/python/feature_vector_generation/src/build_header.py
inst/python/feature_vector_generation/src/build_header.pyc
inst/python/feature_vector_generation/src/build_remarks_for_output_file.py
inst/python/feature_vector_generation/src/build_sequence_feature_vector.py
inst/python/feature_vector_generation/src/build_sequence_feature_vector.pyc
inst/python/feature_vector_generation/src/check.py
inst/python/feature_vector_generation/src/check.pyc
inst/python/feature_vector_generation/src/chemical_signatures.py
inst/python/feature_vector_generation/src/chemical_signatures.pyc
inst/python/feature_vector_generation/src/convert_sequence_to_feature.py
inst/python/feature_vector_generation/src/feature_vector_to_be_printed.py
inst/python/feature_vector_generation/src/feature_vector_to_be_printed.pyc
inst/python/feature_vector_generation/src/five_prime_flanks_MGW_ProT.py
inst/python/feature_vector_generation/src/five_prime_flanks_MGW_ProT.pyc
inst/python/feature_vector_generation/src/five_prime_flanks_Roll_HelT.py
inst/python/feature_vector_generation/src/five_prime_flanks_Roll_HelT.pyc
inst/python/feature_vector_generation/src/hbond_signatures.py
inst/python/feature_vector_generation/src/header_to_be_printed.py
inst/python/feature_vector_generation/src/header_to_be_printed.pyc
inst/python/feature_vector_generation/src/load_alphabets.py
inst/python/feature_vector_generation/src/load_alphabets.pyc
inst/python/feature_vector_generation/src/load_hbond_signatures.py
inst/python/feature_vector_generation/src/load_query_table.py
inst/python/feature_vector_generation/src/load_query_table.pyc
inst/python/feature_vector_generation/src/pentamers_without_flanks_MGW_ProT.py
inst/python/feature_vector_generation/src/pentamers_without_flanks_MGW_ProT.pyc
inst/python/feature_vector_generation/src/pentamers_without_flanks_Roll_HelT.py
inst/python/feature_vector_generation/src/pentamers_without_flanks_Roll_HelT.pyc
inst/python/feature_vector_generation/src/predict_Roll_M.py
inst/python/feature_vector_generation/src/predict_Roll_M.pyc
inst/python/feature_vector_generation/src/predict_Twist_M.py
inst/python/feature_vector_generation/src/predict_Twist_M.pyc
inst/python/feature_vector_generation/src/prediction.py
inst/python/feature_vector_generation/src/rev.py
inst/python/feature_vector_generation/src/rev.pyc
inst/python/feature_vector_generation/src/set_print_options.py
inst/python/feature_vector_generation/src/set_print_options.pyc
inst/python/feature_vector_generation/src/three_prime_flanks_MGW_ProT.py
inst/python/feature_vector_generation/src/three_prime_flanks_MGW_ProT.pyc
inst/python/feature_vector_generation/src/three_prime_flanks_Roll_HelT.py
inst/python/feature_vector_generation/src/three_prime_flanks_Roll_HelT.pyc
inst/python/query_table_analyzer/analyze_diff_qtable.py
inst/python/query_table_analyzer/autoconvert.py
inst/python/query_table_analyzer/autoconvert.pyc
inst/python/query_table_analyzer/check.py
inst/python/query_table_analyzer/check.pyc
inst/python/query_table_analyzer/delta_meth_vs_unmeth.sub
inst/python/query_table_analyzer/load_query_table.py
inst/python/query_table_analyzer/load_query_table.pyc
inst/python/query_table_analyzer/methylate_pentamers_used_in_delta.dat
inst/python/query_table_analyzer/rev_with_M_and_g.py
inst/python/query_table_analyzer/rev_with_M_and_g.pyc
inst/python/query_table_analyzer/unmethylated_pentamers_used_in_delta.dat
inst/python/rev_with_M_and_g.py
satyausc/methylDNAshapeHTmethod documentation built on Dec. 20, 2017, 4:11 a.m.