frma - Frozen RMA and Barcode
Preprocessing and analysis for single microarrays and microarray batches.
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softwaremicroarraypreprocessing
5.70 score 1 dependents 83 scriptsHTqPCR - Automated analysis of high-throughput qPCR data
Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).
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microtitreplateassaydifferentialexpressiongeneexpressiondataimportqualitycontrolpreprocessingvisualizationmultiplecomparisonqpcr
5.06 score 1 dependents 19 scripts 562 downloadsfrmaTools - Frozen RMA Tools
Tools for advanced use of the frma package.
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softwaremicroarraypreprocessing
3.90 score 6 scriptsmiRcomp - Tools to assess and compare miRNA expression estimatation methods
Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.
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softwareqpcrpreprocessingqualitycontrol
3.30 score 2 scriptsternarynet - Ternary Network Estimation
Gene-regulatory network (GRN) modeling seeks to infer dependencies between genes and thereby provide insight into the regulatory relationships that exist within a cell. This package provides a computational Bayesian approach to GRN estimation from perturbation experiments using a ternary network model, in which gene expression is discretized into one of 3 states: up, unchanged, or down). The ternarynet package includes a parallel implementation of the replica exchange Monte Carlo algorithm for fitting network models, using MPI.
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softwarecellbiologygraphandnetworknetworkbayesiancpp
3.30 score 3 scriptsspkTools - Methods for Spike-in Arrays
The package contains functions that can be used to compare expression measures on different array platforms.
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softwaretechnologymicroarray
3.30 score 1 scripts