Platform Design Info for Affymetrix HuGene-1_1-st-v1.

Platform Design Info for NimbleGen 2006-10-31_rn34_refseq_promoter.

Platform Design Info for The Manufacturer's Name Yeast_2.

Platform Design Info for Affymetrix Clariom_S_Human_HT.

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.

This package provides a package containing an environment representing the Poplar.cdf file.

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

Platform Design Info for The Manufacturer's Name HT_HG-U133A.

Platform Design Info for The Manufacturer's Name HC_G110.

Platform Design Info for Affymetrix MTA-1_0.

The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a seamless way for retrieving genomic data from Progenetix database—an open resource dedicated to curated oncogenomic profiles. Empowered by this package, users can effortlessly access and visualize data from Progenetix.

This package contains all the datasets used in the PepsNMR package.

Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 99 vertebrate species.

Affymetrix Affymetrix Porcine Array annotation data (chip porcine) assembled using data from public repositories.

This package provides a package for processing protein mass spectrometry data.

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).

PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs.

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

pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.

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

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 The Manufacturer's Name HG_U95B.

pipeFrame is an R package for building a componentized bioinformatics pipeline. Each step in this pipeline is wrapped in the framework, so the connection among steps is created seamlessly and automatically. Users could focus more on fine-tuning arguments rather than spending a lot of time on transforming file format, passing task outputs to task inputs or installing the dependencies. Componentized step elements can be customized into other new pipelines flexibly as well. This pipeline can be split into several important functional steps, so it is much easier for users to understand the complex arguments from each step rather than parameter combination from the whole pipeline. At the same time, componentized pipeline can restart at the breakpoint and avoid rerunning the whole pipeline, which may save a lot of time for users on pipeline tuning or such issues as power off or process other interrupts.

Platform Design Info for The Manufacturer's Name HG-U133A_tag.