Preview

Sung-Huan-ANNOgesic-6365406
- .gitignore
  
  20 Bytes
- CITATION.cff
  
  477 Bytes
- Dockerfile
  
  7.5 kB
- LICENSE
  
  909 Bytes
- MANIFEST.in
  
  63 Bytes
- Makefile
  
  1.4 kB
- README.rst
  
  6.9 kB
- Table_dependency_version.txt
  
  1.9 kB
- annogesiclib
  - TSS_upstream.py
    
    6.3 kB
  - TSSpredator_parser.py
    
    1.9 kB
  - args_container.py
    
    61.8 kB
  - blast_class.py
    
    1.4 kB
  - change_db_format.py
    
    549 Bytes
  - check_orphan.py
    
    14.2 kB
  - check_srna_overlap.py
    
    3.2 kB
  - circRNA_detection.py
    
    8.3 kB
  - circrna.py
    
    26.1 kB
  - color_png.py
    
    3.9 kB
  - combine_frag_tex.py
    
    3.8 kB
  - combine_gff.py
    
    5.0 kB
  - compare_sRNA_sORF.py
    
    3.3 kB
  - compare_srna_promoter.py
    
    3.3 kB
  - compare_srna_term.py
    
    4.0 kB
  - compare_tran_term.py
    
    7.7 kB
  - controller.py
    
    54.5 kB
  - converter.py
    
    23.2 kB
  - coverage_detection.py
    
    8.1 kB
  - crispr.py
    
    13.8 kB
  - detect_coverage_term.py
    
    24.5 kB
  - detect_operon.py
    
    14.7 kB
  - detect_utr.py
    
    34.3 kB
  - expression.py
    
    3.9 kB
  - extract_RBS.py
    
    8.6 kB
  - extract_psortb.py
    
    6.1 kB
  - extract_sRNA_info.py
    
    12.9 kB
  - extract_sec_info.py
    
    1.2 kB
  - fill_gap.py
    
    8.5 kB
  - filter_TSS_pro.py
    
    1.4 kB
  - filter_low_expression.py
    
    5.1 kB
  - format_fixer.py
    
    4.5 kB
  - gen_TSS_type.py
    
    15.8 kB
  - gen_promoter_table.py
    
    2.3 kB
  - gen_screenshots.py
    
    5.6 kB
  - gen_srna_output.py
    
    17.3 kB
  - gen_svg.py
    
    3.2 kB
  - gen_table_tran.py
    
    7.1 kB
  - gene_express_analysis.py
    
    11.6 kB
  - gene_ontology.py
    
    13.0 kB
  - get_Rfam_ribo.py
    
    993 Bytes
  - get_input.py
    
    3.7 kB
  - get_inter_seq.py
    
    12.8 kB
  - get_polyT.py
    
    17.7 kB
  - get_srna_poly_u.py
    
    6.0 kB
  - get_target_fasta.py
    
    4.5 kB
  - gff3.py
    
    3.4 kB
  - goterm.py
    
    7.8 kB
  - helper.py
    
    15.3 kB
  - lib_reader.py
    
    3.0 kB
  - map_ribos.py
    
    1.6 kB
  - meme.py
    
    21.2 kB
  - merge_feature.py
    
    10.0 kB
  - merge_manual.py
    
    27.7 kB
  - merge_rnaplex_rnaup.py
    
    31.7 kB
  - merge_sRNA.py
    
    24.7 kB
  - modify_rbs_table.py
    
    2.0 kB
  - multiparser.py
    
    17.0 kB
  - operon.py
    
    4.4 kB
  - optimize.py
    
    4.0 kB
  - optimize_TSSpredator.py
    
    44.3 kB
  - output_cutoff_table.py
    
    2.3 kB
  - overlap.py
    
    3.3 kB
  - parser_wig.py
    
    2.1 kB
  - paths.py
    
    25.3 kB
  - plot_PPI.py
    
    10.6 kB
  - plot_TSS_venn.py
    
    6.3 kB
  - plot_coverage_table.py
    
    1.9 kB
  - plot_mountain.py
    
    1.9 kB
  - plot_tran.py
    
    1.4 kB
  - potential_target.py
    
    6.4 kB
  - ppi.py
    
    26.0 kB
  - print_rank_all.py
    
    984 Bytes
  - projectcreator.py
    
    1.0 kB
  - ratt.py
    
    12.7 kB
  - rbs_overlap.py
    
    2.7 kB
  - recompute_RBS.py
    
    8.4 kB
  - reorganize_table.py
    
    2.8 kB
  - ribo_gff.py
    
    7.0 kB
  - ribos.py
    
    16.1 kB
  - sORF_detection.py
    
    46.5 kB
  - sORF_intergenic.py
    
    5.6 kB
  - sRNA_antisense.py
    
    3.4 kB
  - sRNA_class.py
    
    14.2 kB
  - sRNA_filter_frag.py
    
    2.1 kB
  - sRNA_filter_min_utr.py
    
    1.1 kB
  - sRNA_intergenic.py
    
    33.7 kB
  - sRNA_utr_derived.py
    
    37.2 kB
  - screen.py
    
    3.5 kB
  - seq_editer.py
    
    4.1 kB
  - seqmodifier.py
    
    1.6 kB
  - snp.py
    
    16.9 kB
  - sorf.py
    
    9.7 kB
  - splice_parser.py
    
    852 Bytes
  - srna.py
    
    55.1 kB
  - srna_target.py
    
    24.9 kB
  - stat_TA_comparison.py
    
    18.0 kB
  - stat_TSSpredator.py
    
    4.9 kB
  - stat_operon.py
    
    3.8 kB
  - stat_sorf.py
    
    9.0 kB
  - stat_sublocal.py
    
    4.6 kB
  - stat_term.py
    
    11.0 kB
  - sublocal.py
    
    13.1 kB
  - terminator.py
    
    30.4 kB
  - transcript.py
    
    18.0 kB
  - transcript_SNP.py
    
    18.0 kB
  - transcript_detection.py
    
    8.8 kB
  - tsspredator.py
    
    27.3 kB
  - utr.py
    
    4.3 kB
  - validate_gene.py
    
    5.2 kB
- bin
  - annogesic
    
    113.0 kB
- comparison
  - README.md
    
    979 Bytes
  - compare_TSS_Mendoza_Vargas.py
    
    1.6 kB
  - compare_TSS_Salgado.py
    
    2.1 kB
  - compare_operon_door.py
    
    2.6 kB
  - compare_operon_regulondb.py
    
    2.3 kB
  - compare_promoter_regulondb.py
    
    1.7 kB
  - compare_sORF.py
    
    1.7 kB
  - compare_srna.py
    
    2.4 kB
  - compare_term_ecocyc.py
    
    1.6 kB
  - compare_term_regulon.py
    
    2.0 kB
  - compare_tran.py
    
    1.9 kB
  - compare_utr.py
    
    4.1 kB
  - gff3.py
    
    3.3 kB
- database
  - Rfam_RNA_thermometer_ID.csv
    
    576 Bytes
  - Rfam_riboswitch_ID.csv
    
    1.5 kB
  - sRNA_database_BSRD.fa
    
    234.6 kB
- docs
  - Makefile
    
    7.4 kB
  - make.bat
    
    7.3 kB
  - source
    - conf.py
      
      9.3 kB
    - docker.rst
      
      2.8 kB
    - index.rst
      
      5.7 kB
    - installation.rst
      
      2.9 kB
    - license.rst
      
      864 Bytes
    - logo
      - READemption_logo.png
        
        5.4 kB
      - annogesic_logo_white.png
        
        2.3 kB
      - logo_annogesic.pdf
        
        3.9 kB
      - logo_annogesic.png
        
        1.5 kB
    - questions.rst
      
      6.3 kB
    - required.rst
      
      5.2 kB
    - subcommands.rst
      
      198.5 kB
    - tutorial.rst
      
      74.1 kB
    - user_manual.md
      
      9.5 kB
- get_package_database.sh
  
  11.4 kB
- run_test.py
  
  122 Bytes
- setup.py
  
  1.0 kB
- tests
  - mock_args_container.py
    
    70 Bytes
  - mock_gff3.py
    
    1.6 kB
  - mock_helper.py
    
    1.3 kB
  - test_TSSpredator.py
    
    1.7 kB
  - test_blast_class.py
    
    2.6 kB
  - test_change_db_format.py
    
    1.1 kB
  - test_check_orphan.py
    
    12.0 kB
  - test_circRNA.py
    
    10.0 kB
  - test_circrna.py
    
    12.5 kB
  - test_color_png.py
    
    2.4 kB
  - test_combine_frag_tex.py
    
    5.1 kB
  - test_combine_gff.py
    
    10.1 kB
  - test_compare_sRNA_sORF.py
    
    3.9 kB
  - test_converter.py
    
    28.6 kB
  - test_coverage_detection.py
    
    6.5 kB
  - test_detect_coverage_term.py
    
    14.1 kB
  - test_detect_operon.py
    
    10.9 kB
  - test_detect_utr.py
    
    16.1 kB
  - test_expresssion.py
    
    2.8 kB
  - test_extract_RBS.py
    
    5.5 kB
  - test_extract_psortb.py
    
    9.4 kB
  - test_extract_sRNA_info.py
    
    11.6 kB
  - test_fill_gap.py
    
    6.0 kB
  - test_filter_TSS_pro.py
    
    2.6 kB
  - test_filter_low_expression.py
    
    4.7 kB
  - test_format_fixer.py
    
    6.0 kB
  - test_gen_screenshots.py
    
    5.0 kB
  - test_gen_srna_output.py
    
    8.1 kB
  - test_gen_svg.py
    
    2.9 kB
  - test_gen_table_tran.py
    
    2.4 kB
  - test_gene_express_analysis.py
    
    7.3 kB
  - test_gene_ontology.py
    
    15.1 kB
  - test_get_Rfam_ribo.py
    
    3.9 kB
  - test_get_input.py
    
    5.1 kB
  - test_get_inter_seq.py
    
    6.0 kB
  - test_get_polyT.py
    
    6.3 kB
  - test_get_target_fasta.py
    
    4.9 kB
  - test_gff3.py
    
    2.3 kB
  - test_goterm.py
    
    2.6 kB
  - test_helper.py
    
    5.5 kB
  - test_lib_reader.py
    
    6.6 kB
  - test_meme.py
    
    3.4 kB
  - test_merge_manual.py
    
    18.6 kB
  - test_merge_rnaplex_rnaup.py
    
    13.2 kB
  - test_merge_sRNA.py
    
    13.5 kB
  - test_modify_rbs_table.py
    
    1.8 kB
  - test_multiparser.py
    
    10.2 kB
  - test_operon.py
    
    3.6 kB
  - test_optimize.py
    
    3.3 kB
  - test_optimize_TSSpredator.py
    
    26.0 kB
  - test_parser_wig.py
    
    1.8 kB
  - test_paths.py
    
    3.6 kB
  - test_plot_PPI.py
    
    7.5 kB
  - test_plot_TSS_venn.py
    
    3.7 kB
  - test_plot_coverage_table.py
    
    1.1 kB
  - test_plot_mountain.py
    
    1.5 kB
  - test_potential_target.py
    
    6.1 kB
  - test_ppi.py
    
    13.1 kB
  - test_projectcreator.py
    
    1.1 kB
  - test_ratt.py
    
    14.7 kB
  - test_recompute_RBS.py
    
    9.4 kB
  - test_ribo_gff.py
    
    8.0 kB
  - test_ribos.py
    
    20.6 kB
  - test_sORF_detection.py
    
    21.9 kB
  - test_sORF_intergenic.py
    
    3.9 kB
  - test_sRNA_class.py
    
    8.1 kB
  - test_sRNA_intergenic.py
    
    22.3 kB
  - test_sRNA_utr_derived.py
    
    31.3 kB
  - test_screen.py
    
    6.1 kB
  - test_seq_editer.py
    
    2.4 kB
  - test_seqmodifier.py
    
    1.3 kB
  - test_snp.py
    
    10.2 kB
  - test_sorf.py
    
    6.2 kB
  - test_splice_parser.py
    
    1.4 kB
  - test_srna.py
    
    18.8 kB
  - test_srna_target.py
    
    8.9 kB
  - test_stat_TA_comparison.py
    
    12.8 kB
  - test_stat_TSSpredater.py
    
    3.0 kB
  - test_stat_operon.py
    
    4.5 kB
  - test_stat_sorf.py
    
    10.4 kB
  - test_stat_sublocal.py
    
    3.5 kB
  - test_stat_term.py
    
    6.7 kB
  - test_sublocal.py
    
    4.9 kB
  - test_terminator.py
    
    13.9 kB
  - test_transcript.py
    
    11.3 kB
  - test_transcript_SNP.py
    
    21.0 kB
  - test_transcript_detection.py
    
    7.1 kB
  - test_tsspredator.py
    
    18.9 kB
  - test_utr.py
    
    5.7 kB
  - test_validate_gene.py
    
    5.0 kB
  - uni_report.py
    
    1.8 kB
- tutorial_data
  - NC_009839_manual_TSS.gff
    
    9.1 kB
  - mutation.csv
    
    142 Bytes
  - replace_seq_id.py
    
    1.1 kB
  - run.sh
    
    18.6 kB
  - run_with_sigularity.sh
    
    19.8 kB

Sung-Huan/ANNOgesic-v.1.0.1.zip