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Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.
It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.
Platform Design Info for Affymetrix ZebGene-1_1-st.
Platform Design Info for Affymetrix Clariom_D_Human.
Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.
Platform Design Info for The Manufacturer's Name Plasmodium_Anopheles.
Platform Design Info for Affymetrix OviGene-1_1-st.
PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating enrichment score and significance of pathways, and plotting pathways.
Peptide Set Test (PepSetTest) is a peptide-centric strategy to infer differentially expressed proteins in LC-MS/MS proteomics data. This test detects coordinated changes in the expression of peptides originating from the same protein and compares these changes against the rest of the peptidome. Compared to traditional aggregation-based approaches, the peptide set test demonstrates improved statistical power, yet controlling the Type I error rate correctly in most cases. This test can be valuable for discovering novel biomarkers and prioritizing drug targets, especially when the direct application of statistical analysis to protein data fails to provide substantial insights.
Platform Design Info for The Manufacturer's Name X_laevis_2.
Platform Design Info for The Manufacturer's Name HG-U133A_2.
Platform Design Info for The Manufacturer's Name Barley1.
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.
PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: 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.
Account for missing values in label-free mass spectrometry data without imputation. The package implements a probabilistic dropout model that ensures that the information from observed and missing values are properly combined. It adds empirical Bayesian priors to increase power to detect differentially abundant proteins.
Regularization and score distributions for position count matrices.
This package contains data required to run examples in prebs package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer's CDF (manually created using bowtie).
Platform Design Info for Affymetrix EleGene-1_0-st.
Platform Design Info for The Manufacturer's Name HG-U133A_tag.
PartheenMetaData http://swegene.onk.lu.se Annotation Data (PartheenMetaData) assembled using data from public repositories.
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.
The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.
Platform Design Info for The Manufacturer's Name Ecoli.
Polytect is an advanced computational tool designed for the analysis of multi-color digital PCR data. It provides automatic clustering and labeling of partitions into distinct groups based on clusters first identified by the flowPeaks algorithm. Polytect is particularly useful for researchers in molecular biology and bioinformatics, enabling them to gain deeper insights into their experimental results through precise partition classification and data visualization.