Metadata-Version: 2.1
Name: trand
Version: 22.1.6
Summary: 'Transcript Distances'
Home-page: https://github.com/McIntyre-Lab/TranD
Author: McIntyre Lab, Universify of Florida
Author-email: om@rc.ufl.edu
License: MIT
Description: # TranD: Transcript Distances
        
        TranD is a collection of tools to facilitate metrics of structural variation for whole genome
        transcript annotation files (GTF) that pinpoint structural variation to the nucleotide level.
        
        TranD (Transcript Distances) can be used to calculate metrics of structural variation within and
        between annotation files (GTF). Structural variation reflects organismal complexity and three
        summary metrics for genome level complexity are calculated for every gene in a GTF file:  1) the
        number of transcripts per gene; 2) the number of exons per transcript; and 3) the number of
        unique exons (exons with unique genomic coordinates) per gene. From each these metrics
        distributions a summary statistics such as mean, median, variance, inter-quartile range are
        calculated. With 1GTF file input, gene mode can be used to generates these metrics for each gene
        and summary statistics and distributions across genes. Distributions are visualized in a series
        of plots.  For 1 GTF and 2GTF a pairwise mode calculates distance metrics between 2 transcripts
        to the nucleotide.  In 1 GTF this is all possible pairs within the gene and in 2 GTF model this
        is all possible pairs among GTF files. The distribution of these metrics across genes are
        visualized and summary statistics for structural variations between pairs are calculated and
        reported.  Visualizations of the distributions of the frequency of intron retention, alternative
        exon usage, donor/acceptor variation and 5', 3' variation in UTR regions are provided as well as
        tabular formatted nucleotide level distances for both 1GTF and 2 GTF.
        
Keywords: transcript event and distance analysis
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Description-Content-Type: text/markdown
