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

This package is a gene/phenotype prioritization tool that utilizes multiplex heterogeneous gene phenotype network. PhenoGeneRanker allows multi-layer gene and phenotype networks. It also calculates empirical p-values of gene/phenotype ranking using random stratified sampling of genes/phenotypes based on their connectivity degree in the network. https://dl.acm.org/doi/10.1145/3307339.3342155.

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

Platform Design Info for NimbleGen 081229_hg18_promoter_medip_hx1.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Plasmodium\_Anopheles\_probe\_tab.

Platform Design Info for The Manufacturer's Name Pae_G1a.

planttfhunter is used to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification scheme implemented in PlantTFDB. TFs are identified using pre-built hidden Markov model profiles for DNA-binding domains. Then, auxiliary and forbidden domains are used with DNA-binding domains to classify TFs into families and subfamilies (when applicable). Currently, TFs can be classified in 58 different TF families/subfamilies.

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

Most analyses of Affymetrix GeneChip data (including tranditional 3 arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3 arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.

Platform Design Info for The Manufacturer's Name MG_U74Cv2.

The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.

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

Platform Design Info for NimbleGen feinberg_hg18_me_hx1.

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

Platform Design Info for The Manufacturer's Name NuGO_Mm1a520177.

Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter.

This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data.

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

Platform Design Info for Affymetrix MoGene-1_0-st-v1.

Platform Design Info for Affymetrix Clariom_S_Human.

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

Platform Design Info for The Manufacturer's Name MG_U74A.

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

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