gpseq: Using the generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments

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Documentation for package ‘GPseq’ version 0.5

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calc_chisq_statistic Calculate Chi-square goodness of fit Statistic for Generalized Poisson and Poisson Models.
estimate_differential_expression Estimating differential expression statistics for Genes between all possible pairwise conditions
estimate_differential_splicing Estimating differential splicing statistics for an exon in a gene between all possible pairwise conditions
estimate_exon_gene_expression Estimating Exon and Gene Expressions using the Poisson and Generalized Poisson Models and calculating their goodness of fit statistic
exons Exon Annotation Database
generalized_poisson_likelihood Maximum Likelihood Estimates for the Generalized Poisson Model
genes Gene annotations
likelihood_ratio_generalized_poisson_exon_gene Log Likelihood ratio statistic for comparison of the splicing ratio of an exon in two conditions
likelihood_ratio_poisson_exon_gene Log Likelihood ratio statistic for comparison of the splicing ratio of an exon across two conditions using the Poisson Distribution
likelihood_ratio_tissue_generalized_poisson Chi Square test statistic for comparison of expression levels of genes/exons across two conditions using the Generalized Poisson model
likelihood_ratio_tissue_poisson Chi Square test statistic for comparison of expression levels of genes/exons across two conditions using the Poisson Model
perform_permutation_de Perform a Permutation Test to fit the null distribution of the test statistic to a Gamma Distribution
perform_permutation_ds Perform a Permutation Test to fit the null distribution of the test statistic to a Gamma Distribution
reads Mapped Reads