Home ==== .. :Author: Yuanhua Huang .. :Version: 0.2.4 .. :Last viewed: Dec 17, 2016 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. Contents ======== .. toctree:: :maxdepth: 2 install.rst manual.rst example.rst faq.rst release.rst References ---------- Yuanhua Huang and Guido Sanguinetti. `Statistical modeling of isoform splicing dynamics from RNA-seq time series data `_. \ **Bioinformatics**\ (2016) 32 (19): 2965-2972. .. seealso:: SourceForge package: including splicing annotation files http://sourceforge.net/projects/diceseq/files/annotation/ SourceForge package: usage examples http://sourceforge.net/projects/diceseq/files/example/ Splicing event generator: modified from Yarden's rnaseqlib https://github.com/huangyh09/MISO/tree/fastmiso/misopy/events_maker MISO package: Mixture of Isoforms https://miso.readthedocs.io/en/fastmiso/ RNA-seq aligner HISAT https://ccb.jhu.edu/software/hisat/index.shtml Information about pysam http://pysam.readthedocs.org The python language http://www.python.org