DICEseq: Dynamic Isoform spliCing Estimator via sequencing data
Project 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**\. (`under review`_)
.. _under review:
===============================================================
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**\. (`under review`_)
.. _under review:
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