.gitignore
LICENSE
MANIFEST.in
README.md
setup.py
subset.fa
BioSAK/.DS_Store
BioSAK/.RData
BioSAK/.Rhistory
BioSAK/BLCA_op_parser.py
BioSAK/BacDive.py
BioSAK/Barrnap.py
BioSAK/BioSAK_config.py
BioSAK/COG2003.py
BioSAK/COG2014.py
BioSAK/COG2020.py
BioSAK/COG_boxplot_last1row.R
BioSAK/COG_boxplot_last2row.R
BioSAK/CheckM.py
BioSAK/Enrichment.py
BioSAK/FastaSplitler_by_num.py
BioSAK/FastaSplitler_by_size.py
BioSAK/GTDB_for_BLCA.py
BioSAK/Gene2Ctg.py
BioSAK/KEGG.py
BioSAK/KEGG_boxplot_last1row.R
BioSAK/KEGG_get_eukaryotic_kos.py
BioSAK/MeanMappingDepth.py
BioSAK/MetaCHIP_phylo.hmm
BioSAK/MetaCyc_reactions_with_ec.txt
BioSAK/NS_SCG_tree_p_only_group.tree
BioSAK/NS_SCG_tree_p_with_group.tree
BioSAK/NetEnzymes.py
BioSAK/Newick_tree_plotter.py
BioSAK/OneLineAln.py
BioSAK/Prodigal.py
BioSAK/Prokka.py
BioSAK/Reads_simulator.py
BioSAK/SILVA_for_BLCA.py
BioSAK/SankeyTaxon.py
BioSAK/SubsetAlnCols.py
BioSAK/Subset_tree.py
BioSAK/VERSION
BioSAK/VisGeneFlk.py
BioSAK/__init__.py
BioSAK/boxplot_last1row.R
BioSAK/boxplot_matrix_COG.py
BioSAK/boxplot_matrix_COG_backup.py
BioSAK/boxplot_matrix_KEGG.py
BioSAK/cdd2cog.pl
BioSAK/dbCAN.py
BioSAK/download_GenBank_genome.py
BioSAK/download_GenBank_genome_subset_prokaryotes_csv.py
BioSAK/dwnld_sra_reads.py
BioSAK/fa2tree.py
BioSAK/format_converter.py
BioSAK/fq2fa.py
BioSAK/gbk_to_ffn_faa.py
BioSAK/get_EC_from_ko_stats_D.py
BioSAK/get_Pfam_hmms.py
BioSAK/get_SCG_tree.py
BioSAK/get_TopHits_taxonomy.py
BioSAK/get_aa_composition.py
BioSAK/get_bin_abundance.py
BioSAK/get_gc.py
BioSAK/get_gene_depth.py
BioSAK/get_ko_gene_seqs.py
BioSAK/get_reads_from_sam.py
BioSAK/get_sankey_plot.R
BioSAK/get_top_hit.py
BioSAK/get_total_length.py
BioSAK/global_functions.py
BioSAK/iTOL.py
BioSAK/js_cmds.py
BioSAK/keep_best_hit.py
BioSAK/ko00001.keg
BioSAK/label_tree.R
BioSAK/label_tree.py
BioSAK/link_16S_MAG.py
BioSAK/manipulator_fasta.py
BioSAK/manipulator_msa.py
BioSAK/manipulator_newick.py
BioSAK/manipulator_sam.py
BioSAK/mean_MAG_depth.py
BioSAK/ncbi_dataset.py
BioSAK/parse_MetaCyc_RxnDB.py
BioSAK/plot_sam_depth.py
BioSAK/plot_tree.R
BioSAK/reads2bam.py
BioSAK/rename_reads_for_Reago.py
BioSAK/rename_seq.py
BioSAK/sam2bam.py
BioSAK/select_seq.py
BioSAK/sep_reads_by_barcode.py
BioSAK/slice_seq.py
BioSAK/split_folder.py
BioSAK/top_16S_hits.py
BioSAK/usearch_uc.py
BioSAK.egg-info/PKG-INFO
BioSAK.egg-info/SOURCES.txt
BioSAK.egg-info/dependency_links.txt
BioSAK.egg-info/requires.txt
BioSAK.egg-info/top_level.txt
BioSAK/__pycache__/__init__.cpython-35.pyc
BioSAK/__pycache__/__init__.cpython-37.pyc
BioSAK/__pycache__/global_functions.cpython-37.pyc
BioSAK_tutorial/Demo_batch_download_GenBank_genomes/Alteromonas.csv
BioSAK_tutorial/Demo_batch_download_GenBank_genomes/Archaea.csv
BioSAK_tutorial/Demo_batch_download_GenBank_genomes/Demo_batch_download_GenBank_genomes.png
BioSAK_tutorial/Demo_batch_download_GenBank_genomes/README.md
BioSAK_tutorial/Demo_functional_annotation/README.md
BioSAK_tutorial/Demo_functional_annotation/faa_files/NorthSea_bin014.faa
BioSAK_tutorial/Demo_functional_annotation/faa_files/NorthSea_bin022.faa
BioSAK_tutorial/Demo_functional_annotation/faa_files/NorthSea_bin028.faa
BioSAK_tutorial/Demo_functional_annotation/faa_files/NorthSea_bin029.faa
BioSAK_tutorial/Demo_functional_annotation/faa_files/NorthSea_bin034.faa
BioSAK_tutorial/Demo_functional_annotation/ffn_files/NorthSea_bin014.ffn
BioSAK_tutorial/Demo_functional_annotation/ffn_files/NorthSea_bin022.ffn
BioSAK_tutorial/Demo_functional_annotation/ffn_files/NorthSea_bin028.ffn
BioSAK_tutorial/Demo_functional_annotation/ffn_files/NorthSea_bin029.ffn
BioSAK_tutorial/Demo_functional_annotation/ffn_files/NorthSea_bin034.ffn
BioSAK_tutorial/Demo_tree_visualization_with_iTol/README.md
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed.zip
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/colors_dash.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/colors_no_range_tol.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/colors_tol.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/labels.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/popup_info_template.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/ranges.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_alignment.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_binary.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_binary2.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_boxplot.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_color_strip.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_color_strip2.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_connections.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_connections_leaves.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_domains.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_external_shapes.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_gradient.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_heatmap1.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_heatmap60.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_images.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_linechart-sine.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_linechart.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_multibar10.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_multibar50.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_pies1.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_pies2.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_pies3.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_ranges.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_simple_bar.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_simple_bar2.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_simple_bar3.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_styles.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_symbols.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_symbols1.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_symbols2.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_text1.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_text2.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tol_text3.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/Templates_from_iTOL/tree_of_life.tree.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/figures/Layout_Circular.jpg
BioSAK_tutorial/Demo_tree_visualization_with_iTol/figures/Layout_Normal copy.jpg
BioSAK_tutorial/Demo_tree_visualization_with_iTol/figures/Layout_Normal.jpg
BioSAK_tutorial/Demo_tree_visualization_with_iTol/figures/Step_1.jpg
BioSAK_tutorial/Demo_tree_visualization_with_iTol/figures/Step_2.jpg
BioSAK_tutorial/Demo_tree_visualization_with_iTol/figures/Tree_1.jpg
BioSAK_tutorial/Demo_tree_visualization_with_iTol/figures/Tree_2.jpg
BioSAK_tutorial/Demo_tree_visualization_with_iTol/figures/Tree_with_functions_with_size.jpg
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/NorthSea_0_Tree.newick
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/NorthSea_1_Taxon_ColorStrip.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/NorthSea_1_Taxon_Range.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/NorthSea_2_LifeStyle.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/NorthSea_3_Abundance.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/NorthSea_4_MAG_Size.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/Tree_plot_1.pdf
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/Tree_plot_2.pdf
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/Tree_plot_3.pdf
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/raw_data/raw_LifeStyle_color.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/raw_data/raw_MAG_LifeStyle.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/raw_data/raw_MAG_abundance.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/raw_data/raw_MAG_size.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/raw_data/raw_MAG_taxon.txt
BioSAK_tutorial/Demo_tree_visualization_with_iTol/files_needed/raw_data/raw_taxon_color.txt
BioSAK_tutorial/example_files/js_cmds/cmds_gapseq.txt
BioSAK_tutorial/example_files/js_cmds/js_header.txt
My_Python_scripts/.DS_Store
My_Python_scripts/00_Fluent_Python.py
My_Python_scripts/01_file_and_folder.py
My_Python_scripts/02_list_and_dict.py
My_Python_scripts/03_number.py
My_Python_scripts/04_ArgumentParser.py
My_Python_scripts/04_get_color_list.py
My_Python_scripts/04_my_calculator.py
My_Python_scripts/08_parse_combined_CheckM_output.py
My_Python_scripts/10_export_dna_record.py
My_Python_scripts/11_get_defined_region_sequence.py
My_Python_scripts/13_print_time.py
My_Python_scripts/14_pysam_functions.py
My_Python_scripts/15_subsample_unpaired_reads.py
My_Python_scripts/17_subset_tree.py
My_Python_scripts/18_Compare_trees.R
My_Python_scripts/19_parse_combined_checkm_quality.py
My_Python_scripts/20_check_executables.py
My_Python_scripts/21_os_environ.py
My_Python_scripts/22_blast_xml_parser.py
My_Python_scripts/README.md
My_Python_scripts/pandas_drop_small_value_cols_and_rows.py
My_Python_scripts/NetEnzymes/.DS_Store
My_Python_scripts/NetEnzymes/KO2EC.py
My_Python_scripts/NetEnzymes/Prepare_MetaCyc_DB.py
My_Python_scripts/NetEnzymes/Scrapy_MetaCyc.py
My_Python_scripts/NetEnzymes/tmp_1.py
My_Python_scripts/NetEnzymes/.idea/BioNetwork.iml
My_Python_scripts/NetEnzymes/.idea/misc.xml
My_Python_scripts/NetEnzymes/.idea/modules.xml
My_Python_scripts/NetEnzymes/.idea/workspace.xml
My_Python_scripts/NetEnzymes/.idea/inspectionProfiles/profiles_settings.xml
My_Python_scripts/NetEnzymes/__pycache__/pythoncyc.cpython-37.pyc
My_Python_scripts/Pandas_Numpy/Pandas_objects_operation.py
My_Python_scripts/Scrapy/.DS_Store
My_Python_scripts/Scrapy/BeautifulSoup_official.py
My_Python_scripts/Scrapy/data.csv
My_Python_scripts/Scrapy/demo_BaiDu_BaiKe.py
My_Python_scripts/Scrapy/demo_BeautifulSoup.py
My_Python_scripts/Scrapy/demo_KEGG.py
My_Python_scripts/Scrapy/demo_Microbiome.py
My_Python_scripts/Scrapy/demo_download_Microbiome_pdf.py
My_Python_scripts/Scrapy/demo_download_Microbiome_pdf_essential.py
My_Python_scripts/Scrapy/demo_moive_info.py
My_Python_scripts/Scrapy/demo_urllib.py
My_Python_scripts/Scrapy/demo_weather.py
My_Python_scripts/Scrapy/.idea/Scrapy.iml
My_Python_scripts/Scrapy/.idea/encodings.xml
My_Python_scripts/Scrapy/.idea/misc.xml
My_Python_scripts/Scrapy/.idea/modules.xml
My_Python_scripts/Scrapy/.idea/workspace.xml
My_Python_scripts/Scrapy/.idea/libraries/R_User_Library.xml
My_Python_scripts/Scrapy/backup/Scrapy_demo.py
My_Python_scripts/Scrapy/backup/beautifulsoup4_demo.py
My_Python_scripts/Scrapy/backup/toscrape-css.py
My_Python_scripts/Scrapy/backup/toscrape-xpath.py
My_Python_scripts/Stats_with_python/Bonferroni_correction.py
My_Python_scripts/Stats_with_python/Normality_test.py
My_Python_scripts/TCG/LICENSE.txt
My_Python_scripts/TCG/README.md
My_Python_scripts/TCG/TCG.py
My_Python_scripts/TCG/get_db.py
My_Python_scripts/TCG/db_files/bac120.HMM.gz
My_Python_scripts/TCG/images/Krona_plot.png
My_Python_scripts/TCG/images/TCG.jpg
My_Python_scripts/TCG/images/TCG_logo.jpg
My_Python_scripts/TCG/manual/How_TCG_works.pdf
My_Python_scripts/TCG/manual/run_example.zip
My_Python_scripts/TCG/tmp/Test_1.py
My_Python_scripts/TCG/tmp/Test_2.py
My_Python_scripts/comparative_genomics/COG(need_improvement).py
My_Python_scripts/comparative_genomics/COG_number_count.py
My_Python_scripts/comparative_genomics/Core_genome.py
My_Python_scripts/comparative_genomics/gene_function_file_for_PGAP.py
My_Python_scripts/comparative_genomics/put_each_orthology_in_one_line.py
My_Python_scripts/for_plot/Boxplot_with_extra_values.png
My_Python_scripts/for_plot/Boxplot_with_extra_values.py
My_Python_scripts/for_plot/Grouped_boxplot_with_extra_values.csv
My_Python_scripts/for_plot/Grouped_boxplot_with_extra_values.png
My_Python_scripts/for_plot/Grouped_boxplot_with_extra_values.py
My_Python_scripts/for_plot/README.md
My_Python_scripts/for_plot/add_text_to_image.py
My_Python_scripts/for_plot/basic_barplot.png
My_Python_scripts/for_plot/basic_boxplot.png
My_Python_scripts/for_plot/basic_plot.py
My_Python_scripts/for_plot/boxplot_with_dots.png
My_Python_scripts/for_plot/boxplot_with_dots.py
My_Python_scripts/for_plot/categorical_scatter_plot.png
My_Python_scripts/for_plot/color_palettes.py
My_Python_scripts/for_plot/customized_subplots.png
My_Python_scripts/for_plot/customized_subplots.py
My_Python_scripts/for_plot/grouped_boxplot.png
My_Python_scripts/for_plot/grouped_boxplot.py
My_Python_scripts/for_plot/plot/.DS_Store
My_Python_scripts/for_plot/plot/2D_line.png
My_Python_scripts/for_plot/plot/2D_line.py
My_Python_scripts/for_plot/plot/2D_scatter_1.png
My_Python_scripts/for_plot/plot/2D_scatter_1.py
My_Python_scripts/for_plot/plot/2D_scatter_2_dot_size.png
My_Python_scripts/for_plot/plot/2D_scatter_2_dot_size.py
My_Python_scripts/for_plot/plot/2D_scatter_3_groups.png
My_Python_scripts/for_plot/plot/2D_scatter_3_groups.py
My_Python_scripts/for_plot/plot/3D_scatter.png
My_Python_scripts/for_plot/plot/3D_scatter.py
My_Python_scripts/for_plot/plot/Add_text_in_matplotlib.png
My_Python_scripts/for_plot/plot/Add_text_in_matplotlib.py
My_Python_scripts/for_plot/plot/Chord_Diagram_plotter.py
My_Python_scripts/for_plot/plot/Density_plot_gaussian_kde.png
My_Python_scripts/for_plot/plot/Density_plot_gaussian_kde.py
My_Python_scripts/for_plot/plot/Distribution_plot_4_in_1.png
My_Python_scripts/for_plot/plot/Distribution_plot_4_in_1.py
My_Python_scripts/for_plot/plot/Heatmap_in_ploty.png
My_Python_scripts/for_plot/plot/Heatmap_in_ploty.py
My_Python_scripts/for_plot/plot/README.md
My_Python_scripts/for_plot/plot/add_text_to_image.py
My_Python_scripts/for_plot/plot/bar_plotter.py
My_Python_scripts/for_plot/plot/box_plotter.py
My_Python_scripts/for_plot/plot/box_plotter_with_dots.png
My_Python_scripts/for_plot/plot/box_plotter_with_dots.py
My_Python_scripts/for_plot/plot/plot_boxplot_with_dots.py
My_Python_scripts/tree_related/Newick_tree_plotter.py
My_Python_scripts/tree_related/Test_88.py
My_Python_scripts/tree_related/test_10_Phylo_demo.py
My_Python_scripts/tree_related/test_14.py
My_Python_scripts/tree_related/test_3.py
My_Python_scripts/tree_related/tree_2_matrix.py
My_Python_scripts/tree_related/tree_ploter.py
My_R_scripts/.DS_Store
My_R_scripts/.Rhistory
My_R_scripts/Learning_R.R
My_R_scripts/README.md
My_R_scripts/demo.R
My_R_scripts/demo_01_data_structure.R
My_R_scripts/demo_02_list_manipulation.R
My_R_scripts/demo_03_ESBL.csv
My_R_scripts/demo_03_dataframe_manipulation.R
My_R_scripts/demo_04_check_packages.R
My_R_scripts/demo_05_file_IO.R
My_R_scripts/demo_06_folders_and_files.R
My_R_scripts/demo_07_seqinr.R
My_R_scripts/demo_SRAdb.R
My_R_scripts/demo_tmp1.R
My_R_scripts/demo_tmp2.R
My_R_scripts/demo_tmp3.R
My_R_scripts/getresiduals-gc.R
My_R_scripts/important_R.R
My_R_scripts/plot_export_format.R
My_R_scripts/Environmental_Computing_tutorials/.Rhistory
My_R_scripts/Environmental_Computing_tutorials/Generalised_linear_model_1.R
My_R_scripts/Environmental_Computing_tutorials/Generalised_linear_model_2.R
My_R_scripts/Environmental_Computing_tutorials/Generalised_linear_model_3_Interpreting_coefficients.R
My_R_scripts/Environmental_Computing_tutorials/Introduction_to_mvabund.R
My_R_scripts/Environmental_Computing_tutorials/T1_T-tests_One_sample_t-tests.R
My_R_scripts/Environmental_Computing_tutorials/T2_T-tests_Independent_samples_t-tests.R
My_R_scripts/Environmental_Computing_tutorials/T3_T-tests_Paired_t-tests.R
My_R_scripts/Environmental_Computing_tutorials/T4_Linear_models_Linear_regression.R
My_R_scripts/Environmental_Computing_tutorials/data/Crabs.csv
My_R_scripts/Environmental_Computing_tutorials/data/Greenhouse.csv
My_R_scripts/Environmental_Computing_tutorials/data/Herbivore_specialisation.csv
My_R_scripts/Environmental_Computing_tutorials/data/Revegetation.csv
My_R_scripts/Environmental_Computing_tutorials/data/River_pH.csv
My_R_scripts/Plot_examples/.DS_Store
My_R_scripts/Plot_examples/.RData
My_R_scripts/Plot_examples/.Rhistory
My_R_scripts/Plot_examples/COG_summary_boxplot_last1row.R
My_R_scripts/Plot_examples/COG_summary_boxplot_last1row_smart.R
My_R_scripts/Plot_examples/COG_summary_boxplot_last2row.R
My_R_scripts/Plot_examples/Circlize_demo.R
My_R_scripts/Plot_examples/Circlize_demo_2.R
My_R_scripts/Plot_examples/Circlize_demo_2.png
My_R_scripts/Plot_examples/Circlize_demo_grouped.R
My_R_scripts/Plot_examples/README.md
My_R_scripts/Plot_examples/Two-way_scatter_plot.R
My_R_scripts/Plot_examples/Two-way_scatter_plot.png
My_R_scripts/Plot_examples/VennDiagram.R
My_R_scripts/Plot_examples/VennDiagram.png
My_R_scripts/Plot_examples/boxplot_last1row.R
My_R_scripts/Plot_examples/demo_R_color_list.R
My_R_scripts/Plot_examples/demo_R_color_list.png
My_R_scripts/Plot_examples/diptest.R
My_R_scripts/Plot_examples/gapminder_2016.csv
My_R_scripts/Plot_examples/gapminder_2016_dot.R
My_R_scripts/Plot_examples/gapminder_2016_dot.png
My_R_scripts/Plot_examples/ggplot_heatmap.R
My_R_scripts/Plot_examples/googleVis.R
My_R_scripts/Plot_examples/googleVis.jpg
My_R_scripts/Plot_examples/googleVis_example_data copy.csv
My_R_scripts/Plot_examples/googleVis_example_data.csv
My_R_scripts/Plot_examples/googlevis_input.csv
My_R_scripts/Plot_examples/heatmap_plotrix.R
My_R_scripts/Plot_examples/heatmap_plotrix.png
My_R_scripts/Plot_examples/heatmap_plotrix_example_data.csv
My_R_scripts/Plot_examples/heatmap_ploty.R
My_R_scripts/Plot_examples/heatmap_ploty_1.png
My_R_scripts/Plot_examples/heatmap_ploty_2.png
My_R_scripts/Plot_examples/heatmap_with_tree.R
My_R_scripts/Plot_examples/plot_ggplot2.R
My_R_scripts/Plot_examples/plot_ggplot2_1.png
My_R_scripts/Plot_examples/plot_ggplot2_2.png
My_R_scripts/Plot_examples/plot_ggplot2_3.png
My_R_scripts/Plot_examples/undone/Untitled copy.R
My_R_scripts/Plot_examples/undone/Untitled.R
My_R_scripts/Plot_examples/undone/Untitled.Rmd
My_R_scripts/Plot_examples/undone/Untitled.html
My_R_scripts/Plot_examples/undone/igraph.R
My_R_scripts/Plot_examples/undone/micropan.R
My_R_scripts/Plot_examples/undone/migest_commands.R
My_R_scripts/Plot_examples/undone/networkD3.R
My_R_scripts/Stats_in_R/.DS_Store
My_R_scripts/Stats_in_R/.RData
My_R_scripts/Stats_in_R/.Rhistory
My_R_scripts/Stats_in_R/stats_ANOVA.R
My_R_scripts/Stats_in_R/stats_Dissimilarity_stats.R
My_R_scripts/Stats_in_R/stats_Diversity_stats.R
My_R_scripts/Stats_in_R/stats_Linear_Regression.R
My_R_scripts/Stats_in_R/stats_Linear_Regression_DataCamp.R
My_R_scripts/Stats_in_R/stats_MDS.R
My_R_scripts/Stats_in_R/stats_Normality_test.R
My_R_scripts/Stats_in_R/stats_One_Sample_T_test.R
My_R_scripts/Stats_in_R/stats_One_Sample_Wilcoxon_test.R
My_R_scripts/Stats_in_R/stats_One_way_ANOVA .R
My_R_scripts/Stats_in_R/stats_T-test_and_Correlation-test.R
My_R_scripts/Stats_in_R/stats_Vegan_Procrustes_analysis.R
My_R_scripts/Stats_in_R/stats_subsample_STATS.R
My_R_scripts/Stats_in_R/ToDo/stats_Kruskal_Wallis_test.R
My_R_scripts/Stats_in_R/ToDo/stats_Logistic_Regression.R
My_R_scripts/Stats_in_R/ToDo/stats_Logistic_Regression_DataCamp.R
My_R_scripts/Stats_in_R/ToDo/stats_MANOVA.R
My_R_scripts/Stats_in_R/ToDo/stats_Two_way_ANOVA.R
My_R_scripts/Tmp/ICoVeR.R
My_R_scripts/Tmp/Untitled copy 2.R
My_R_scripts/Tmp/Untitled copy.R
My_R_scripts/Tmp/Untitled2.R
My_R_scripts/Tmp/pastecs.R
My_R_scripts/Tree_manipulation/.DS_Store
My_R_scripts/Tree_manipulation/.Rhistory
My_R_scripts/Tree_manipulation/Combine_Tree_HeatMap.R
My_R_scripts/Tree_manipulation/Compare_trees.R
My_R_scripts/Tree_manipulation/Tree2grouping.R
My_R_scripts/Tree_manipulation/add_group_to_tree.R
My_R_scripts/Tree_manipulation/cluster_distance.R
My_R_scripts/Tree_manipulation/subset_tree.R
My_R_scripts/deepSNV/.Rhistory
My_R_scripts/deepSNV/deepSNV_example.R
My_R_scripts/deepSNV/deepSNV_flow_cell_biofilm.R
My_R_scripts/deepSNV/get_SNVs.R
bin/BioSAK
bin/__init__.py
images/.DS_Store
images/Bioinformatics.jpg
images/windows_cmds.docx
images/windows_cmds.pdf
tmp_scripts/COG_summary_heatmap.py
tmp_scripts/Common_stop_codon_sequence_generator.py
tmp_scripts/Display_progress_bar.py
tmp_scripts/Generate_matrix_list.py
tmp_scripts/Get_crosslink.py
tmp_scripts/Get_reads_subset.py
tmp_scripts/InPrep1_Prokka.py
tmp_scripts/InPrep3_Get_SCG_tree.py
tmp_scripts/InPrep_Get_homologues.py
tmp_scripts/NCBI_taxonomy_Extract_interested_taxon_from_nodes_and_names_files.py
tmp_scripts/NCBI_taxonomy_get_ancestors.py
tmp_scripts/Phylogenetic_back.py
tmp_scripts/Test_6666_3.py
tmp_scripts/Test_get_average_distance.py
tmp_scripts/Test_this_one.py
tmp_scripts/chemical_solution_calculator.py
tmp_scripts/cluster_from_msa.py
tmp_scripts/cluster_to_grouping_file.py
tmp_scripts/get_anvio_binning_results.py
tmp_scripts/get_average_coverage.py
tmp_scripts/get_coverage_from_sam.py
tmp_scripts/get_distance_matirx.py
tmp_scripts/get_reads_from_sam.py
tmp_scripts/get_total_reads_length.py
tmp_scripts/hmmerWrapper.py
tmp_scripts/hmmerWrapper_updated.py
tmp_scripts/node_colormap.png
tmp_scripts/plot_cross_link.py
tmp_scripts/plot_gene_and_gc_track_in_GenomeDiagram.py
tmp_scripts/qsub_file_generator_katana.py
tmp_scripts/remove_unpaired_reads.py
tmp_scripts/rpy.py
tmp_scripts/simple_path.png
tmp_scripts/split_paired_reads.py
tmp_scripts/test_1.py
tmp_scripts/test_16_get_failed_prediction.py
tmp_scripts/test_2.py
tmp_scripts/test_3.py
tmp_scripts/test_4_googleVis.py
tmp_scripts/test_5.py
tmp_scripts/test_6_get_core_genes.py
tmp_scripts/test_sankey.py
tmp_scripts/tmp_1.py
tmp_scripts/tmp_2.py
tmp_scripts/tmp_3.py
tmp_scripts/tmp_4.py
tmp_scripts/tmp_5.py
tmp_scripts/tmp_6.py
tmp_scripts/tmp_7.py
tmp_scripts/tmp_8.py
tmp_scripts/tmp_9.py