Preview

rouskinlab-seismic-rna-b1ca4ef
- .github
  - workflows
    - gh-pages.yml
      
      370 Bytes
    - test-src.yml
      
      1.4 kB
- .gitignore
  
  2.1 kB
- CITATION.cff
  
  431 Bytes
- DEV-MANUAL.pdf
  
  167.0 kB
- INSTALL.md
  
  1.1 kB
- LICENSE
  
  35.1 kB
- README.md
  
  1.3 kB
- SCHEDULE.md
  
  3.2 kB
- USER-MANUAL.md
  
  7.0 kB
- VENV.md
  
  5.2 kB
- docs
  - dev
    - src
      - _all.sh
        
        284 Bytes
      - _build.sh
        
        237 Bytes
      - _clean.sh
        
        366 Bytes
      - main.tex
        
        2.0 kB
      - refs.bib
        
        0 Bytes
      - title.tex
        
        2.6 kB
  - user
    - make.sh
      
      421 Bytes
    - src
      - about
        
        authors.rst
        
        635 Bytes
        
        dms.rst
        
        767 Bytes
        
        dreem.rst
        
        88 Bytes
        
        index.rst
        
        247 Bytes
        
        license.rst
        
        717 Bytes
      - algos
        
        index.rst
        
        157 Bytes
      - api
        
        seismicrna.align.rst
        
        529 Bytes
        
        seismicrna.align.tests.rst
        
        286 Bytes
        
        seismicrna.cluster.rst
        
        940 Bytes
        
        seismicrna.core.rst
        
        2.3 kB
        
        seismicrna.core.tests.rst
        
        588 Bytes
        
        seismicrna.demult.rst
        
        361 Bytes
        
        seismicrna.fold.rst
        
        352 Bytes
        
        seismicrna.graph.rst
        
        1.2 kB
        
        seismicrna.mask.rst
        
        533 Bytes
        
        seismicrna.relate.rst
        
        1.0 kB
        
        seismicrna.relate.tests.rst
        
        283 Bytes
        
        seismicrna.rst
        
        505 Bytes
        
        seismicrna.sim.rst
        
        132 Bytes
        
        seismicrna.table.rst
        
        636 Bytes
        
        seismicrna.test.rst
        
        251 Bytes
      - cli.rst
        
        1.0 kB
      - conf.py
        
        3.0 kB
      - data
        
        index.rst
        
        188 Bytes
        
        relate.rst
        
        11.1 kB
        
        relationships.pdf
        
        227.8 kB
        
        relationships.png
        
        53.7 kB
      - formats
        
        data
        
        fastq.rst
        
        5.2 kB
        
        index.rst
        
        132 Bytes
        
        relate.rst
        
        168 Bytes
        
        sam.rst
        
        261 Bytes
        
        index.rst
        
        225 Bytes
        
        reports
        
        cluster.rst
        
        2.4 kB
        
        index.rst
        
        139 Bytes
        
        relate.rst
        
        2.4 kB
      - index.rst
        
        403 Bytes
      - install
        
        conda.rst
        
        5.2 kB
        
        index.rst
        
        223 Bytes
        
        prereqs.rst
        
        3.7 kB
        
        venv.rst
        
        6.0 kB
      - manuals
        
        index.rst
        
        202 Bytes
        
        logging.rst
        
        5.8 kB
        
        steps
        
        align.rst
        
        14.2 kB
        
        all.rst
        
        630 Bytes
        
        index.rst
        
        141 Bytes
      - tutorials
        
        amplicon.rst
        
        231 Bytes
        
        example.rst
        
        4.6 kB
        
        index.rst
        
        196 Bytes
- env.yml
  
  183 Bytes
- example
  - sars2-fse_R1.fq.gz
    
    11.3 MB
  - sars2-fse_R2.fq.gz
    
    13.0 MB
  - sars2.fa
    
    295 Bytes
- flowchart.png
  
  179.5 kB
- flowchart.pptx
  
  39.4 kB
- logo-48.png
  
  3.8 kB
- logo.png
  
  111.3 kB
- logo.py
  
  7.0 kB
- logo_test.py
  
  207 Bytes
- pyproject.toml
  
  1.2 kB
- src
  - seismicrna
    - __init__.py
      
      2.0 kB
    - align
      - README.md
        
        1.6 kB
      - __init__.py
        
        543 Bytes
      - fq2bam.py
        
        23.1 kB
      - fqutil.py
        
        19.6 kB
      - main.py
        
        7.8 kB
      - tests
        
        __init__.py
        
        0 Bytes
        
        fqutil_test.py
        
        4.8 kB
    - cluster
      - README.md
        
        3.1 kB
      - __init__.py
        
        35 Bytes
      - compare.py
        
        9.8 kB
      - em.py
        
        24.2 kB
      - krun.py
        
        6.3 kB
      - load.py
        
        4.2 kB
      - main.py
        
        2.6 kB
      - names.py
        
        1.3 kB
      - report.py
        
        2.9 kB
      - write.py
        
        4.9 kB
    - core
      - __init__.py
        
        0 Bytes
      - bitcall.py
        
        15.8 kB
      - bitvect.py
        
        25.7 kB
      - cli.py
        
        18.7 kB
      - cmd.py
        
        558 Bytes
      - depend.py
        
        1.1 kB
      - docdef.py
        
        6.8 kB
      - files.py
        
        628 Bytes
      - load.py
        
        7.9 kB
      - logs.py
        
        4.5 kB
      - mu.py
        
        22.6 kB
      - pair.py
        
        10.5 kB
      - parallel.py
        
        14.6 kB
      - path.py
        
        24.2 kB
      - rel.py
        
        35.9 kB
      - report.py
        
        29.7 kB
      - rna.py
        
        8.7 kB
      - sect.py
        
        26.4 kB
      - seq.py
        
        11.3 kB
      - shell.py
        
        2.8 kB
      - sim.py
        
        235 Bytes
      - subcls.py
        
        758 Bytes
      - tests
        
        __init__.py
        
        0 Bytes
        
        mu_test.py
        
        29.7 kB
        
        rel_test.py
        
        56.8 kB
        
        sect_test.py
        
        8.8 kB
        
        seq_test.py
        
        11.4 kB
      - xam.py
        
        14.4 kB
    - demult
      - __init__.py
        
        35 Bytes
      - demultiplex.py
        
        42.6 kB
      - main.py
        
        2.1 kB
    - fold
      - __init__.py
        
        35 Bytes
      - main.py
        
        3.9 kB
      - rnastructure.py
        
        1.8 kB
    - graph
      - __init__.py
        
        22 Bytes
      - base.py
        
        11.2 kB
      - color.py
        
        3.5 kB
      - main.py
        
        476 Bytes
      - scatter.py
        
        3.2 kB
      - seq.py
        
        1.6 kB
      - seqbar.py
        
        10.0 kB
      - seqcorr.py
        
        3.9 kB
      - seqdiff.py
        
        1.4 kB
      - seqpair.py
        
        13.7 kB
      - traces.py
        
        4.1 kB
      - write.py
        
        2.7 kB
    - main.py
      
      11.6 kB
    - mask
      - __init__.py
        
        35 Bytes
      - load.py
        
        4.1 kB
      - main.py
        
        4.4 kB
      - report.py
        
        1.3 kB
      - write.py
        
        14.2 kB
    - relate
      - README.md
        
        16.5 kB
      - __init__.py
        
        35 Bytes
      - export.py
        
        1.4 kB
      - load.py
        
        3.2 kB
      - main.py
        
        3.2 kB
      - relate.c
        
        28.4 kB
      - relate.py
        
        27.5 kB
      - report.py
        
        1.5 kB
      - sam.py
        
        8.2 kB
      - seqpos.py
        
        3.0 kB
      - tests
        
        __init__.py
        
        0 Bytes
        
        test.py
        
        3.1 kB
      - write.py
        
        14.8 kB
    - sim
      - __init__.py
        
        0 Bytes
    - table
      - __init__.py
        
        35 Bytes
      - base.py
        
        9.0 kB
      - load.py
        
        8.5 kB
      - main.py
        
        2.2 kB
      - tabulate.py
        
        15.7 kB
      - write.py
        
        4.7 kB
    - test
      - __init__.py
        
        147 Bytes
      - main.py
        
        1.3 kB

rouskinlab/seismic-rna-v0.7.0.zip