Metadata-Version: 1.0
Name: diceseq
Version: 0.2.3
Summary: DICEseq: Dynamic Isoform spliCing Estimator via sequencing data
Home-page: http://diceseq.sourceforge.net
Author: Yuanhua Huang
Author-email: Y.Huang@ed.ac.uk
License: MIT
Description: DICEseq: Dynamic Isoform spliCing Estimator via sequencing data
        ===============================================================
        
        About DICEseq
        -------------
        
        DICEseq (Dynamic Isoform spliCing Estimator via sequencing data) estimates the dynamics of isoform proportions jointly from time series RNA-seq experiments. DICEseq is a Bayesian method based on a mixture model whose mixing proportions represent isoform ratios. It incorporates the correlations from the temporal structure, by coupling the isoform proportions at different times through a latent Gaussian process (GP).
        
        DICEseq provides following functions through command line:
        
        1. ``diceseq``: 
        
        * Estimate the isoform proportions and FPKM jointly or separately. 
        * Calculate the Bayes factor to detect the differential dynamics of splicing profile.
        
        2. ``dice-count``: 
        
        * Get the total reads counts of each gene. 
        * Get the specific reads counts, e.g., junction reads, for genes with exactly one intron. This is particularly design for yeast.
        
        3. ``dice-bias``: 
        
        * Estimate fragment length distribution.
        * Estimate reads sequence and position bias parameter. The output file can be directly used for bias correction in ``diceseq``.
        
        In addition, DICEseq package also provides interface of a set of functions and attributes as an object-oriented python module. Therefore, you could use some of the module e.g., ``SampleFile`` to visualize the samples in gzip file in a Gaussian process way, or ``BiasFile`` to visualize the bias parameters. Also, the ``gtf_utils`` provides a set of ways to load gtf file, choose the genes, or customize the coordinates of exons and introns, add and remove of specific transcripts.
        
        More information
        ----------------
        
        See the documentation_ on how to install, to use, to find the annotation data etc.
        
        .. _documentation: http://diceseq.sourceforge.net
        
        
        References
        ----------
        
        Yuanhua Huang and Guido Sanguinetti. `Statistical modeling of isoform splicing dynamics from RNA-seq time series data 
        <http://bioinformatics.oxfordjournals.org/content/32/19/2965.abstract>`_. \ **Bioinformatics**\, 2016, 32(19): 2965-2972.
        
Keywords: splicing isoform quantification,time series RNA-seq,Gaussian process,Markov chain Monte Carlo
Platform: UNKNOWN
