The Disperse project aims to develop and distribute software and data for design of selector assays for exon resequencing applications. The software consists of Java and Perl code integrated into a pipeline that performs all tasks required to transform a list of gene names to a set of selector probes targetting all exonic regions of those genes
CFAssay provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.
::DEVELOPER
Herbert Braselmann <braselm at helmholtz-muenchen.de>
MRMPlusGUI is a freely available, open-source tool in the platform independent Java programming language to compute analytical measures as recommended recently by the Clinical Proteomics Tumor Analysis Consortium Assay Development Working Group for “Tier 2” assays.
PROBer is the first unified probabilistic framework for the analysis of a diverse set of sequencing-based ‘toeprinting’ assays. These assays are used to probe RNA secondary structure (DMS/SHAPE-Seq), detect epitranscriptomic mark (Pseudo-Seq), or identify RNA-protein interaction (iCLIP/eCLIP), which are important to understanding post-transcriptional gene regulation from all aspects.
MethMarker facilitates the design of DNA methylation assays for COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight and MSP. It also implements a systematic workflow for design, optimization and (computational) validation of DNA methylation biomarkers. This workflow starts from a preselected differentially methylated region (DMR) and results in an optimized DNA methylation assay that is ready to be tested in a large-scale clinical trial.
fitTetra is an R package for genotype calling of tetraploid samples based on bi-allelic marker assays such as Illumina GoldenGate, Infinium and KASPar. The main characteristic of such assays is that they produce two signals for a sample for a given marker, one signal for each of the two alleles.
AssayZap is a universal assay calculator for RIA, ELISA, IRMA, colorimetric or any other type of assay. Counts of up to 2^31 can be handled. Standard curves can be fitted by 2-parameter, 4-parameter or 4-parameter weighted fit, or by the unique interactive manual fit which permits all standard curves to be fitted, whatever their shape. Assays may include up to 2000 tubes and up to four standard curves, each of which can incorporate up to 24 values. Assay drift can be compensated by interpolation of results between standard curves.