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Provides easy to use, objective oriented functions for preprocessing methylation data produced by an Illumina Infinium BeadChip and detecting differentially methylated positions and regions within the DNA.
A selection of analytical approaches, tools, and utilities for the processing of microbiome data derived from either 16S rRNA amplicon sequencing or shotgun metagenomics.
Timeseries analysis of -omics data can be carried out by fitting spline curves to the data and using limma for hypothesis testing. For this, the right spline freedom and further hyperparameters must be identified, and the obtained hits clustered based on the spline shape.The R package SplineOmics streamlines this whole process and generates reports
The Tasmanian devil is endangered due to Devil Facial Tumour Disease (DFTD), a contagious cancer with no current treatment. Previous study has investigated the anticancer properties of Tasmanian devil cathelicidins. This report intends to reproduce the enrichment analysis results of the study and further analyze their data.
This scripts involves five major steps including GEO dataset download, data normalization, data manipulation, fetching phenodata and feature data and differentially expressed genes (DEGs) analysis using R and bioconductor packages.
Normalization, outlier detection, statistical analysis, and visualization of microarray data from 79 tumor samples to identify differentially expressed genes between recurrent and non-recurrent prostate cancer.