beer - Bayesian Enrichment Estimation in R
BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data. Given a PhIPData object, BEER returns posterior probabilities of enriched antibody responses, point estimates for the relative fold-change in comparison to negative control samples, and more. Additionally, BEER provides a convenient implementation for using edgeR to identify enriched antibody responses.
Last updated 24 days ago
softwarestatisticalmethodbayesiansequencingcoverage
5.33 score 9 stars 12 scripts 152 downloadsPhIPData - Container for PhIP-Seq Experiments
PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.
Last updated 24 days ago
infrastructuredatarepresentationsequencingcoverage
5.18 score 5 stars 1 packages 6 scripts 174 downloads