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This package provides a tool that enables in silico identification, integration, and modeling of mRNA features that influence post-transcriptional regulation of gene expression at a transcriptome-wide scale.
Platform Design Info for The Manufacturer's Name Barley1.
PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs.
Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).
Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.
Platform Design Info for NimbleGen charm_hg18_example.
Platform Design Info for The Manufacturer's Name HG-U133A_tag.
Platform Design Info for Affymetrix Mapping250K_Nsp.
ProteoMM is a statistical method to perform model-based peptide-level differential expression analysis of single or multiple datasets. For multiple datasets ProteoMM produces a single fold change and p-value for each protein across multiple datasets. ProteoMM provides functionality for normalization, missing value imputation and differential expression. Model-based peptide-level imputation and differential expression analysis component of package follows the analysis described in “A statistical framework for protein quantitation in bottom-up MS based proteomics" (Karpievitch et al. Bioinformatics 2009). EigenMS normalisation is implemented as described in "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition." (Karpievitch et al. Bioinformatics 2009).
Platform Design Info for Affymetrix RJpGene-1_1-st.
Platform Design Info for Affymetrix HTA-2_0.
Platform Design Info for Affymetrix Clariom_D_Human.
This package provides functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.
Platform Design Info for The Manufacturer's Name Drosophila_2.
Platform Design Info for NimbleGen 2006-10-31_rn34_refseq_promoter.
Platform Design Info for Affymetrix FelGene-1_0-st.
Platform Design Info for Affymetrix CHOGene-2_0-st.
Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter.
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 for processing protein mass spectrometry data.
Platform Design Info for Affymetrix miRNA-4_0.
Platform Design Info for Affymetrix Clariom_S_Mouse.
Platform Design Info for The Manufacturer's Name Rice.
Platform Design Info for Affymetrix RTA-1_0.