Platform Design Info for The Manufacturer's Name HG_U95Av2.

Platform Design Info for Affymetrix CynGene-1_1-st.

Platform Design Info for The Manufacturer's Name Tomato.

Platform Design Info for Affymetrix FinGene-1_0-st.

Platform Design Info for The Manufacturer's Name RAE230A.

This is a package that includes pre-processing and quality control functions that can remove margin events, compensate and transform the data and that will use PeacoQCSignalStability for quality control. This last function will first detect peaks in each channel of the flowframe. It will remove anomalies based on the IsolationTree function and the MAD outlier detection method. This package can be used for both flow- and mass cytometry data.

piRNAs (short for PIWI-interacting RNAs) and their PIWI protein partners play a key role in fertility and maintaining genome integrity by restricting mobile genetic elements (transposons) in germ cells. piRNAs originate from genomic regions known as piRNA clusters. The piRNA Cluster Builder (PICB) is a versatile toolkit designed to identify genomic regions with a high density of piRNAs. It constructs piRNA clusters through a stepwise integration of unique and multimapping piRNAs and offers wide-ranging parameter settings, supported by an optimization function that allows users to test different parameter combinations to tailor the analysis to their specific piRNA system. The output includes extensive metadata columns, enabling researchers to rank clusters and extract cluster characteristics.

Platform Design Info for Affymetrix EleGene-1_0-st.

Platform Design Info for The Manufacturer's Name wheat.

This package provides a Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset.

Platform Design Info for Affymetrix miRNA-3_1.

ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.

Platform Design Info for The Manufacturer's Name HG_U95B.

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).

Platform Design Info for The Manufacturer's Name YG_S98.

Platform Design Info for The Manufacturer's Name NuGO_Hs1a520180.

This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.

Platform Design Info for Affymetrix MoGene-2_0-st.

Platform Design Info for Affymetrix ZebGene-1_1-st.

Platform Design Info for Affymetrix RabGene-1_1-st.

This package contains all the datasets used in the PepsNMR package.

Package for the position related analysis of quantitative functional genomics data.

Platform Design Info for Affymetrix GenomeWideSNP_5.