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.
  1. 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.
  1. 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.