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

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Some functions for modeling sequence read counts as a generalized poisson model and to use this model for detecting differentially expressed genes in different conditions and differentially spliced exons.

Author
Sudeep Srivastava, Liang Chen
Date of publication
2011-07-06 18:55:51
Maintainer
Sudeep Srivastava <sudeepsr@usc.edu>
License
GPL-2
Version
0.5

View on CRAN

Man pages

calc_chisq_statistic
Calculate Chi-square goodness of fit Statistic for...
estimate_differential_expression
Estimating differential expression statistics for Genes...
estimate_differential_splicing
Estimating differential splicing statistics for an exon in a...
estimate_exon_gene_expression
Estimating Exon and Gene Expressions using the Poisson and...
exons
Exon Annotation Database
generalized_poisson_likelihood
Maximum Likelihood Estimates for the Generalized Poisson...
genes
Gene annotations
likelihood_ratio_generalized_poisson_exon_gene
Log Likelihood ratio statistic for comparison of the splicing...
likelihood_ratio_poisson_exon_gene
Log Likelihood ratio statistic for comparison of the splicing...
likelihood_ratio_tissue_generalized_poisson
Chi Square test statistic for comparison of expression levels...
likelihood_ratio_tissue_poisson
Chi Square test statistic for comparison of expression levels...
perform_permutation_de
Perform a Permutation Test to fit the null distribution of...
perform_permutation_ds
Perform a Permutation Test to fit the null distribution of...
reads
Mapped Reads

Files in this package

GPseq
GPseq/R
GPseq/R/genpseq.R
GPseq/R/wrapper2.R
GPseq/R/wrapper3.R
GPseq/R/wrapper1.R
GPseq/scr
GPseq/DESCRIPTION
GPseq/man
GPseq/man/likelihood_ratio_tissue_generalized_poisson.Rd
GPseq/man/perform_permutation_ds.Rd
GPseq/man/calc_chisq_statistic.Rd
GPseq/man/exons.Rd
GPseq/man/reads.Rd
GPseq/man/likelihood_ratio_generalized_poisson_exon_gene.Rd
GPseq/man/estimate_exon_gene_expression.Rd
GPseq/man/estimate_differential_splicing.Rd
GPseq/man/likelihood_ratio_tissue_poisson.Rd
GPseq/man/estimate_differential_expression.Rd
GPseq/man/generalized_poisson_likelihood.Rd
GPseq/man/genes.Rd
GPseq/man/likelihood_ratio_poisson_exon_gene.Rd
GPseq/man/perform_permutation_de.Rd
GPseq/NAMESPACE
GPseq/doc
GPseq/data
GPseq/data/genes.rda
GPseq/data/exons.rda
GPseq/data/reads.rda