Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).

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

This package provides a simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.

Platform Design Info for The Manufacturer's Name HG-Focus.

This package provides a GUI interface for the DAPAR package. The package Prostar (Proteomics statistical analysis with R) is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required.

Platform Design Info for Affymetrix Atdschip_tiling.

PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.

Platform Design Info for The Manufacturer's Name Ecoli_ASv2.

Platform Design Info for The Manufacturer's Name Vitis_Vinifera.

Platform Design Info for The Manufacturer's Name miRNA-1_0.

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

FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories.

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.

Platform Design Info for The Manufacturer's Name NuGO_Mm1a520177.

PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs.

This package provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV.

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

Relative transcript abundance has proven to be a valuable tool for understanding the function of genes in biological systems. For the differential analysis of transcript abundance using RNA sequencing data, the negative binomial model is by far the most frequently adopted. However, common methods that are based on a negative binomial model are not robust to extreme outliers, which we found to be abundant in public datasets. So far, no rigorous and probabilistic methods for detection of outliers have been developed for RNA sequencing data, leaving the identification mostly to visual inspection. Recent advances in Bayesian computation allow large-scale comparison of observed data against its theoretical distribution given in a statistical model. Here we propose ppcseq, a key quality-control tool for identifying transcripts that include outlier data points in differential expression analysis, which do not follow a negative binomial distribution. Applying ppcseq to analyse several publicly available datasets using popular tools, we show that from 3 to 10 percent of differentially abundant transcripts across algorithms and datasets had statistics inflated by the presence of outliers.

Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0).

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

Base annotation databases for pig, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

Platform Design Info for The Manufacturer's Name Yeast_2.

Platform Design Info for The Manufacturer's Name Porcine.

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