GitHub

Most of our open-source tools and tutorials (including this website) can be found on the statOmics organization on GitHub.

1. Software Tools
   • stageR: stage-wise testing for gene-level FDR control
   • zingeR: zero inflated negative binomial gene expression in R
   • MSqRob: Robust peptide level models for differential analysis in proteomics
   • SAAS: Search all assess subset, Reliable Peptide Identification when interested in a subset, SAAS Documentation, SAAS Online tool
2. Courses
   • Proteomics Data Analysis
   • Proteomics Data Analysis (2018), Gulbenkian Training Programme in Bioinformatics
3. Companion repositories with the Data Analysis of Journal Papers
   • Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications. Genome Biology 2018 19(1):24, PMID: 29478411
   • stageR, stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biology 2017 18(1):151PMID: 28784146
   • Model based classification for digital PCR: your umbrella for rain. Analytical Chemistry 2017 18;89(8):4461-4467. PMID: 28350455

Bioconductor

1. StatOmics packages
   • stageR
   • waveTiling
2. Contributions to
   • MSnbase
   • unifiedWMWqPCR
   • ZINB-WaVE