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This package provides a general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019.
Platform Design Info for Affymetrix ChiGene-1_1-st.
This package provides a Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.
Platform Design Info for The Manufacturer's Name Mu11KsubB.
Platform Design Info for The Manufacturer's Name Mu11KsubA.
Platform Design Info for The Manufacturer's Name Canine.
Platform Design Info for Affymetrix AraGene-1_1-st.
This package provides a data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples.
This package provides a comprehensive set of external and internal evaluation metrics. It includes metrics for assessing partitions or fuzzy partitions derived from clustering results, as well as for evaluating subpopulation identification results within embeddings or graph representations. Additionally, it provides metrics for comparing spatial domain detection results against ground truth labels, and tools for visualizing spatial errors.
Platform Design Info for Affymetrix RabGene-1_0-st.
Platform Design Info for Affymetrix EleGene-1_0-st.
The Parallel Mixed Model (PMM) approach is suitable for hit selection and cross-comparison of RNAi screens generated in experiments that are performed in parallel under several conditions. For example, we could think of the measurements or readouts from cells under RNAi knock-down, which are infected with several pathogens or which are grown from different cell lines.
This package provides a Bioconductor data package for the Taylor et al (2010) dataset.
Platform Design Info for Affymetrix GenomeWideSNP_5.
Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis.
High-throughput omics data are often affected by systematic biases introduced throughout all the steps of a clinical study, from sample collection to quantification. Normalization methods aim to adjust for these biases to make the actual biological signal more prominent. However, selecting an appropriate normalization method is challenging due to the wide range of available approaches. Therefore, a comparative evaluation of unnormalized and normalized data is essential in identifying an appropriate normalization strategy for a specific data set. This R package provides different functions for preprocessing, normalizing, and evaluating different normalization approaches. Furthermore, normalization methods can be evaluated on downstream steps, such as differential expression analysis and statistical enrichment analysis. Spike-in data sets with known ground truth and real-world data sets of biological experiments acquired by either tandem mass tag (TMT) or label-free quantification (LFQ) can be analyzed.
This package provides a function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.
Platform Design Info for Affymetrix CHOGene-2_1-st.
Platform Design Info for Affymetrix Clariom_S_Rat.
Platform Design Info for The Manufacturer's Name HT_HG-U133_Plus_PM.
PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs.
Platform Design Info for The Manufacturer's Name Sugar_Cane.
This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J., Source Code for Biology and Medicine 2012 Sep 24;7(1):10.
Platform Design Info for Affymetrix RaGene-2_0-st.