Preview

bsmith89-smith2018paper-f05bc03
- .gitattributes
  
  82 Bytes
- .gitignore
  
  415 Bytes
- Makefile
  
  28.9 kB
- README.md
  
  3.9 kB
- doc
  - bibliography.bib
    
    182.3 kB
  - preprint.tex
    
    87.5 kB
  - static
    - acarbose_structure.svg
      
      43.3 kB
    - concept-diagram.pdf
      
      204.5 kB
  - template
    - bmc-mathphys.bst
      
      61.1 kB
    - bmcart-nofigbox.cls
      
      55.7 kB
- matplotlibrc
  
  13 Bytes
- meta
  - extraction.tsv
    
    10.6 kB
  - hplc
    - calibration_config.tsv
      
      529 Bytes
    - calibration_group.tsv
      
      24.5 kB
    - injection.tsv
      
      28.8 kB
    - known.tsv
      
      2.0 kB
    - molecule.tsv
      
      398 Bytes
    - standard.tsv
      
      2.0 kB
  - misc
    - bacteroidales.silva.seed.meta.tsv
      
      20.1 kB
    - bacteroidales_family_designation.tsv
      
      847 Bytes
    - bacteroidales_ref.silva.antipattern.list
      
      238 Bytes
    - bacteroidales_ref.silva.pattern.list
      
      4.6 kB
    - custom_ref_seqs.fn
      
      1.6 kB
  - mouse.tsv
    
    7.6 kB
  - rrs
    - analysis_group.tsv
      
      2.1 kB
    - library.tsv
      
      8.2 kB
    - primer.tsv
      
      145 Bytes
    - spike.fn
      
      2.9 kB
  - sample.tsv
    
    7.1 kB
  - spike.tsv
    
    115 Bytes
- nb
  - bacteroidales_phylo.ipynb
    
    14.3 kB
  - jupyter_notebook_config.py
    
    135 Bytes
  - main_results.ipynb
    
    58.4 kB
  - muribac_uniq.ipynb
    
    12.8 kB
  - otu_details.ipynb
    
    21.8 kB
  - profile_default
    - ipython_kernel_config.py
      
      246 Bytes
  - survival_analysis.ipynb
    
    20.5 kB
- raw
  - hplc
    - 2015-12-19.RI.lcs_export.txt
      
      155.7 kB
    - 2015-12-20.RI.lcs_export.txt
      
      136.8 kB
    - 2015-12-30_a.RI.lcs_export.txt
      
      193.3 kB
    - 2016-01-08_c.RI.lcs_export.txt
      
      158.3 kB
    - 2016-01-24.RI.lcs_export.txt
      
      138.9 kB
    - 2016-02-26_a.RI.lcs_export.txt
      
      100.0 kB
    - 2016-02-26_b.RI.lcs_export.txt
      
      115.3 kB
    - 2016-05-08.RI.lcs_export.txt
      
      340.5 kB
    - 2016-05-15.RI.lcs_export.txt
      
      321.7 kB
    - 2016-05-18.RI.lcs_export.txt
      
      110.2 kB
    - 2016-06-28.RI.lcs_export.txt
      
      377.5 kB
    - proto
      - 2016-01-08_b.RI.lcs_export.txt
        
        223.1 kB
      - 2016-01-26.RI.lcs_export.txt
        
        319.8 kB
      - 2016-03-10.RI.lcs_export.txt
        
        106.4 kB
      - 2016-05-11.RI.lcs_export.txt
        
        425.4 kB
- requirements.pip
  
  338 Bytes
- schema_metadata.sql
  
  9.8 kB
- schema_results.sql
  
  9.5 kB
- scripts
  - __init__.py
    
    0 Bytes
  - calibrate_hplc.py
    
    2.3 kB
  - concat_tables.py
    
    568 Bytes
  - generate_rrs_makefile.py
    
    1.2 kB
  - get_groups.sh
    
    337 Bytes
  - get_ordered_leaves.py
    
    279 Bytes
  - import_db.py
    
    1.9 kB
  - ipynb_output_filter.py
    
    435 Bytes
  - lib
    - __init__.py
      
      0 Bytes
    - data.py
      
      5.9 kB
    - plotting.py
      
      9.3 kB
    - stats.py
      
      1.5 kB
  - otus_to_names_file.py
    
    673 Bytes
  - parse_lcs_export.py
    
    3.2 kB
  - parse_names_as_taxonomy.py
    
    626 Bytes
  - parse_otu_taxonomy.py
    
    1.5 kB
  - pbs
    - interactive.pbs
      
      144 Bytes
    - make.all.pbs
      
      1.3 kB
  - pivot_count_table.py
    
    703 Bytes
  - plot_hplc_calibration.py
    
    4.1 kB
  - qc_hplc.py
    
    1.5 kB
  - squeeze_alignment.py
    
    993 Bytes
  - stack_shared.py
    
    780 Bytes

bsmith89/smith2018paper-v1.1.zip