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

Platform Design Info for Affymetrix HuEx-1_0-st-v2.

Platform Design Info for The Manufacturer's Name MG_U74Av2.

This package provides a package containing an environment representing the Pae_G1a.CDF file.

Platform Design Info for The Manufacturer's Name NuGO_Mm1a520177.

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

Platform Design Info for The Manufacturer's Name Plasmodium_Anopheles.

Platform Design Info for The Manufacturer's Name DrosGenome1.

This package provides a Bioconductor data package for the Grasso (2012) Prostate Cancer dataset.

Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC.

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

Platform Design Info for Affymetrix Clariom_S_Human.

Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA-seq in the context of differential expression (DE), this topic in the field of single-cell RNA sequencing is understudied. Moreover, the unique data characteristics present in scRNA-seq such as sparsity and heterogeneity increase the challenge. We propose POWSC, a simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship.

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 The Manufacturer's Name HC_G110.

Platform Design Info for The Manufacturer's Name Cotton.

pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.

Platform Design Info for Affymetrix DroGene-1_1-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.

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

Platform Design Info for The Manufacturer's Name Bsubtilis.

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

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

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.