Platform Design Info for Affymetrix Clariom_S_Mouse_HT.

It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.

Platform Design Info for Affymetrix Clariom_S_Rat.

CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.

PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.

The PIUMA package offers a tidy pipeline of Topological Data Analysis frameworks to identify and characterize communities in high and heterogeneous dimensional data.

Platform Design Info for The Manufacturer's Name HT_HG-U133_Plus_PM.

Platform Design Info for NimbleGen feinberg_hg18_me_hx1.

This package provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al.

Platform Design Info for The Manufacturer's Name X_laevis_2.

Platform Design Info for The Manufacturer's Name wheat.

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 PrimeView\_probe\_tab.

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

Platform Design Info for Affymetrix RTA-1_0.

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.

Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 99 vertebrate species.

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

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

This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: 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.

Reads files exported from QX Manager or QuantaSoft containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.

This package provides support for parallelized estimation of GLMs/GEEs, catering for dispersed data.

PrInCE (Predicting Interactomes from Co-Elution) uses a naive Bayes classifier trained on dataset-derived features to recover protein-protein interactions from co-elution chromatogram profiles. This package contains the R implementation of PrInCE.

Platform Design Info for The Manufacturer's Name Canine.

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.