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This package provides a package for processing protein mass spectrometry data.
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).
Platform Design Info for Affymetrix RCnGene-1_0-st.
The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.
Affymetrix Affymetrix Porcine Array annotation data (chip porcine) assembled using data from public repositories.
FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories.
Platform Design Info for Affymetrix HuGene-2_1-st.
This package provides support for parallelized estimation of GLMs/GEEs, catering for dispersed data.
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.
This package provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al.
Platform Design Info for Affymetrix miRNA-3_1.
This package provides a shiny app-based GUI wrapper for ggplot with built-in statistical analysis. Import data from file and use dropdown menus and checkboxes to specify the plotting variables, graph type, and look of your plots. Once created, plots can be saved independently or stored in a report that can be saved as a pdf. If new data are added to the file, the report can be refreshed to include new data. Statistical tests can be selected and added to the graphs. Analysis of flow cytometry data is especially integrated with plotGrouper. Count data can be transformed to return the absolute number of cells in a sample (this feature requires inclusion of the number of beads per sample and information about any dilution performed).
Platform Design Info for Affymetrix FinGene-1_1-st.
This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.
Platform Design Info for The Manufacturer's Name Rat230_2.
Platform Design Info for The Manufacturer's Name wheat.
Platform Design Info for The Manufacturer's Name Bovine.
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.
Platform Design Info for The Manufacturer's Name MG_U74B.
Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter.
Platform Design Info for The Manufacturer's Name Yeast_2.
Platform Design Info for The Manufacturer's Name S_aureus.
Pviz adapts the Gviz package for protein sequences and data.
Platform Design Info for The Manufacturer's Name Drosophila_2.