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:
diceseq
:dice-count
:dice-bias
: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.
Yuanhua Huang and Guido Sanguinetti. Statistical modeling of isoform splicing dynamics from RNA-seq time series data. Bioinformatics(2016) 32 (19): 2965-2972.
See also