RNAMAP2D is a software to the analysis of contact maps of RNA structures and protein – RNA complexes. The program deals with modified base pairs which are very frequent in RNA and includes ligands and ions which plays key roles in forming and stabilizing RNA structures. What is more, it is possible to show on the computed map whether some of the identified contacts are recognized as belonging to one of the 12 base pairs families, are canonical Watson – Crick pairs, or are 4 classes of stacking interactions. The overlap of the 2D maps of two structures can be easily calculated, providing a measure of RNA structure similarity.
TDFragMapper can deal with multiple fragmentation methods and can rapidly highlight the experimental fragmentation parameters that are critical to the characterization of intact proteins of various size using top-down proteomics.
ProteinVR is a web-based application that allows users to view protein/ligand structures in virtual reality (VR) from their mobile, desktop, or VR-headset-based web browsers. Molecular structures are displayed within 3D environments that give useful biological context and allow users to situate themselves in 3D space.
V-Phaser is a tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. V-Phaser combines information regarding the covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity.
V-Profiler takes a read alignment and a list of accepted variants at each location in the alignment (such as would be generated by V-Phaser) and analyzes the intra-host diversity of a genome. This can be done at the nucleotide level over the whole sequence, at the codon level for each gene specified in a list, and at the haplotype level for any region delimited (note that the region must not exceed a read length, and is preferably of shorter length such as an epitope or a loop of interest).
CRISPRO is a pipeline to process next generation sequnecing data from saturating mutagenesis CRISPR screens, whereby sgRNAs are mapped to amino acids of the protein, allowing for the inference of functional scores for amino acids in a protein.
Avatar features interactively customizable alteration plots, extensive data import capabilities and a multi-objective optimization algorithm to find alteration patterns, e.g. gene sets with mutually exclusive alterations or small gene sets with high sample coverage.
IdeogramBrowser was specifically designed for use with the Affymetrix SNP arrays. It provides an interactive karyotypic visualization of multiple aberration profiles and direct links to GeneCards.
spatialTIME (Spatial Analysis of Vectra Immunoflourescent Data) is to perform basic analysis and plotting of IF data from Vectra.
iTIME (interactive Tumor Immune MicroEnvironment) is a shiny application that creates interactive figures for examining spatial organization of individual tumors and provide basic spatial and summary information.
Helium is a generic platform in which various data types can be shown in a pedigree context and we hope to have a beta version available soon that users can download and experiment with.