This section documents the modules used in CGAT scripts.
These are the modules that every script or module should use.
.. toctree:: :maxdepth: 1 modules/Experiment.rst modules/IOTools.rst
Modules for parsing and working for data in specific formats.
.. toctree:: :maxdepth: 1 modules/AGP.rst modules/BamTools.rst modules/Bed.rst modules/Biomart.rst modules/Blat.rst modules/CBioPortal.rst modules/FastaIterator.rst modules/Fastq.rst modules/GFF3.rst modules/GTF.rst modules/IndexedFasta.rst modules/IndexedGenome.rst modules/Maq.rst modules/Sra.rst modules/VCF.rst
.. toctree:: :maxdepth: 1 modules/AString.rst modules/Counts.rst modules/Expression.rst modules/GO.rst modules/Genomics.rst modules/Intervals.rst modules/Mali.rst modules/Motifs.rst modules/SequencePairProperties.rst modules/SequenceProperties.rst modules/Variants.rst
These modules wrap tools and provide routines for parsing their output.
.. toctree:: :maxdepth: 1 modules/WrapperCodeML.rst modules/WrapperMuscle.rst modules/Bioprospector.rst modules/WrapperIDR.rst modules/WrapperMACS.rst modules/WrapperZinba.rst modules/MAST.rst modules/Glam2.rst modules/Glam2Scan.rst modules/Tophat.rst modules/IGV.rst modules/LCA.rst modules/Metaphlan.rst modules/Diamond.rst modules/Masker.rst
.. toctree:: :maxdepth: 1 modules/CorrespondenceAnalysis.rst modules/Histogram.rst modules/Histogram2D.rst modules/Stats.rst modules/MatlabTools.rst modules/MatrixTools.rst
Toolboxes for generic problems.
.. toctree:: :maxdepth: 1 modules/CSV.rst modules/Iterators.rst modules/Database.rst modules/SetTools.rst modules/Tree.rst modules/TreeTools.rst
Below is a list of modules that are involved in maintainig the CGAT infrastructure such as logging, dependency tracking, etc.
.. toctree:: :maxdepth: 1 modules/Requirements.rst modules/Style.rst modules/Logfile.rst modules/CSV2DB.rst
.. toctree:: :maxdepth: 1 modules/RLE.rst modules/SVGdraw.rst modules/RateEstimation.rst
Modules not sorted into categories.
.. toctree:: :maxdepth: 2