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Platform Design Info for Affymetrix GuiGene-1_0-st.
Platform Design Info for Affymetrix GenomeWideSNP_5.
Platform Design Info for Affymetrix MarGene-1_1-st.
Platform Design Info for Affymetrix PorGene-1_0-st.
The ProteinGymR package provides analysis-ready data resources from ProteinGym, generated by Notin et al., 2023, as well as built-in functionality to visualize the data. ProteinGym comprises a collection of benchmarks for evaluating the performance of models predicting the effect of point mutations. This package provides access to 1. deep mutational scanning (DMS) scores from 217 assays measuring the impact of all possible amino acid substitutions across 186 proteins, 2. model performance metrics and prediction scores from 79 variant prediction models in the zero-shot setting and 12 models in the semi-supervised setting.
Platform Design Info for Affymetrix CyRGene-1_0-st.
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.
Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 99 vertebrate species.
Platform Design Info for Affymetrix RJpGene-1_1-st.
This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.
Platform Design Info for The Manufacturer's Name MOE430B.
This package calculates probabilistic pathway scores using gene expression data. Gene expression values are aggregated into pathway-based scores using Bayesian network representations of biological pathways.
Regularization and score distributions for position count matrices.
Platform Design Info for The Manufacturer's Name Drosophila_2.
Platform Design Info for NimbleGen 081229_hg18_promoter_medip_hx1.
PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.
Platform Design Info for The Manufacturer's Name MG_U74B.
PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs.
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 Affymetrix RaGene-2_0-st.
Platform Design Info for The Manufacturer's Name Medicago.
Platform Design Info for Affymetrix Clariom_S_Mouse.
PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.
Platform Design Info for Affymetrix RTA-1_0.