Biocview "Preprocessing"

A "corrective make-up" program for microarray chips
A "corrective make-up" program for microarray chips
Adaptive Robust Regression normalization for Illumina methylation data
Adaptive Robust Regression normalization for Illumina methylation data
Adjust for positional and batch effects using ComBat
A fast scatterplot smoother suitable for microarray normalization
A fast scatterplot smoother suitable for microarray normalization
Affymetrix Quality Assessment and Analysis Tool
Affymetrix Quality Assessment and Analysis Tool
A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
A generic R plugin dispatcher for BASE
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
All sample mean normalization.
ALS for the Automatic Chemical Exploration of mixtures
ALS for the Automatic Chemical Exploration of mixtures
ALS for the Automatic Chemical Exploration of mixtures
alternative CDF environments (aka probeset mappings)
alternative CDF environments (aka probeset mappings)
A model for network-based prioritisation of genes
A model for network-based prioritisation of genes
A model for network-based prioritisation of genes
Analysis of Agilent Microarray Data [draft]
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analysis of cell-based screens - revised version of cellHTS
Analysis of cell-based screens - revised version of cellHTS
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
Analysis of high-throughput microscopy-based screens
Analysis of high-throughput microscopy-based screens
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
Analysis of Illumina microarray data [A DRAFT - TRUE]
Analysis of Large Affymetrix Microarray Data Sets
Analysis of Large Affymetrix Microarray Data Sets
Analyze and correct probe positional bias in microarray data due to RNA degradation
Analyze and correct probe positional bias in microarray data due to RNA degradation
Analyze Illumina Infinium DNA methylation arrays
Analyze Illumina Infinium DNA methylation arrays
Analyze Illumina Infinium DNA methylation arrays
An R Object-oriented Microarray Analysis package
An R package for RNA visualization and analysis
An R package for RNA visualization and analysis
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
An R package for the creation of complex genomic profile plots
An R package for the creation of complex genomic profile plots
An R package for the creation of complex genomic profile plots
An R package for the creation of complex genomic profile plots
An R package of Data Importing, Processing and Analysis for Opera High Content Screening System
An R package of Data Importing, Processing and Analysis for Opera High Content Screening System
a package for checking high-throughput genomic data redundancy in meta-analysis
a package for checking high-throughput genomic data redundancy in meta-analysis
A package for the analysis of GC-MS metabolite profiling data
A package for the analysis of GC-MS metabolite profiling data
A package for the clinical proteomic profiling data analysis
A package for the clinical proteomic profiling data analysis
A test for when to use quantile normalization
A test for when to use quantile normalization
A test for when to use quantile normalization
A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
Automated analysis of high-throughput qPCR data
Automated analysis of high-throughput qPCR data
Background Adjustment Using Sequence Information
Background Adjustment Using Sequence Information
Basic graphic utilities for visualization of genomic data.
Basic graphic utilities for visualization of genomic data.
Batch Effects Quality Control Software
Batch Effects Quality Control Software
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Binomial test for Hi-C data analysis
Binomial test for Hi-C data analysis
Calibration model for estimating absolute expression levels from microarray data
Calibration model for estimating absolute expression levels from microarray data
Calling aberrations for array CGH tumor profiles.
Calling aberrations for array CGH tumor profiles.
Calling aberrations for array CGH tumor profiles.
CDF Environment Maker
CDF Environment Maker
CGH Micro-Array NORmalization
CGH Micro-Array NORmalization
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
Conditional quantile normalization
Conditional quantile normalization
Convenience package for solving some liftover challenges
Convenience package for solving some liftover challenges
Convert miRNA Names to Different miRBase Versions
Convert miRNA Names to Different miRBase Versions
Convert the GatingSet from Boost serialization to protocol buffer format
Copy-Number Analysis of Large Microarray Data Sets
Copy-Number Analysis of Large Microarray Data Sets
Copy number information from targeted sequencing using off-target reads
Copy number information from targeted sequencing using off-target reads
Copy number information from targeted sequencing using off-target reads
Copy number information from targeted sequencing using off-target reads
Copy number prediction with correction for GC and mappability bias for HTS data
Copy number prediction with correction for GC and mappability bias for HTS data
Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Count summarization and normalization for RNA-Seq data
Count summarization and normalization for RNA-Seq data
Cross Platform Meta-Analysis of Microarray Data
Cross Platform Meta-Analysis of Microarray Data
Cross Platform Meta-Analysis of Microarray Data
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
Data-driven normalization strategies for high-throughput qPCR data.
Data-driven normalization strategies for high-throughput qPCR data.
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
DeepBlueR
DeepBlueR
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detection of focal aberrations in DNA copy number data
Detection of focal aberrations in DNA copy number data
Differential Analyis of Hi-C Data
Differential Analyis of Hi-C Data
Differential Analyis of Hi-C Data
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
Easy extraction of individual probes in Affymetrix tiling arrays
Efficient algorithms for DNA methylation
Efficient compression and analysis of Hi-C Data
Empirical Bayes estimate of block diagonal covariance matrices
Empirical Bayes estimate of block diagonal covariance matrices
Empirical Bayes estimate of block diagonal covariance matrices
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Estimate Pairwise Interactions from multidimensional features
Estimate Pairwise Interactions from multidimensional features
Excluding host reads from xenograft sequencing data
Exploratory analysis for two-color spotted microarray data
Exploratory analysis for two-color spotted microarray data
Exploratory Data Analysis and Normalization for RNA-Seq
Exploratory Data Analysis and Normalization for RNA-Seq
Exploratory Data Analysis and Normalization for RNA-Seq
FARMS - Factor Analysis for Robust Microarray Summarization
FARMS - Factor Analysis for Robust Microarray Summarization
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Filter replicated high-throughput transcriptome sequencing data
Filter replicated high-throughput transcriptome sequencing data
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Frozen RMA and Barcode
Frozen RMA and Barcode
Frozen RMA Tools
Frozen RMA Tools
Functions to handle cDNA microarray data, including several methods of data analysis
Functions to handle cDNA microarray data, including several methods of data analysis
Functions to process LM-PCR reads from 454/Illumina data
Functions to process LM-PCR reads from 454/Illumina data
Gaussian Process Ranking and Estimation of Gene Expression time-series
Gaussian Process Ranking and Estimation of Gene Expression time-series
Gaussian Process Ranking and Estimation of Gene Expression time-series
geneChip Analysis Package
geneChip Analysis Package
Gene network reconstruction
Gene network reconstruction
Gene-Specific Phenotype EstimatoR
Gene-Specific Phenotype EstimatoR
Gene-Specific Phenotype EstimatoR
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Graphical user interface for OLIN
Graphical user interface for OLIN
Graphics Toolbox for Assessment of Affymetrix Expression Measures
Graphics Toolbox for Assessment of Affymetrix Expression Measures
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
GUI for limma package with Affymetrix microarrays
GUI for limma package with Affymetrix microarrays
GUI for limma package with two color microarrays
GUI for limma package with two color microarrays
Handle Illumina methylation data
Handle Illumina methylation data
Handle Illumina methylation data
Helper functions for creating a MultiAssayExperiment instance with TCGA data
Helper functions for creating a MultiAssayExperiment instance with TCGA data
Helper functions for creating a MultiAssayExperiment instance with TCGA data
Hierarchical Gating Pipeline for flow cytometry data
Hierarchical Gating Pipeline for flow cytometry data
High-Throughput Sequence Analysis using the Aroma Framework
Hits Selection for Synthetic Lethal RNAi Screen Data
Hits Selection for Synthetic Lethal RNAi Screen Data
HIV Annotation
Identify Differentially Expressed Genes from RNA-seq data
Identify Differentially Expressed Genes from RNA-seq data
Identifying differential DNA loops from chromatin topology data
Identifying differential DNA loops from chromatin topology data
Identifying differential DNA loops from chromatin topology data
Illumina 450 methylation array normalization and metrics
Illumina 450 methylation array normalization and metrics
Illumina methylation array analysis for large experiments
Illumina methylation array analysis for large experiments
Illumina methylation array analysis for large experiments
Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay"
Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay"
Infrastructure for representing and interacting with the gated cytometry
Infrastructure for representing and interacting with the gated cytometry
integrated Bayesian Modeling of eQTL data
integrated Bayesian Modeling of eQTL data
integrated Bayesian Modeling of eQTL data
Interactive visualization for Illumina methylation arrays
Interactive visualization for Illumina methylation arrays
Interactive visualization for Illumina methylation arrays
IP-seq data analysis and vizualization
IP-seq data analysis and vizualization
Iteratively Adjusted Surrogate Variable Analysis
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Linear Model of background subtraction and the Langmuir isotherm
Linear Model of background subtraction and the Langmuir isotherm
Linear Models for Microarray Data
Linear Models for Microarray Data
Linear Models for Microarray Data
LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
LVS normalization for Agilent miRNA data
LVS normalization for Agilent miRNA data
Manipulation of Codelink microarray data
Manipulation of Codelink microarray data
MBCB (Model-based Background Correction for Beadarray)
MBCB (Model-based Background Correction for Beadarray)
Methods for Affymetrix Oligonucleotide Arrays
Methods for Affymetrix Oligonucleotide Arrays
Methods for fitting probe-level models
Methods for fitting probe-level models
Methylation Enriched LOci Normalization (MELON) for genome-wide DNA methylation experiments
MiChip Parsing and Summarizing Functions
MiChip Parsing and Summarizing Functions
Microarray Analysis of Differential Expression
Microarray Analysis tool
Microarray Analysis tool
Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.
Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.
Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
Murine Palate miRNA Expression Analysis
Murine Palate miRNA Expression Analysis
Non-detects in qPCR data
Non-detects in qPCR data
Non-detects in qPCR data
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Normalization and reporting of Illumina SNP bead arrays
Normalization and reporting of Illumina SNP bead arrays
Normalization of array CGH data with imbalanced aberrations.
Normalization of array CGH data with imbalanced aberrations.
Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
Optimized local intensity-dependent normalisation of two-color microarrays
Optimized local intensity-dependent normalisation of two-color microarrays
Package analyse 4C sequencing data
Package analyse 4C sequencing data
Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays
Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays
Perform a maximum contrast projection of 3D images along the z-dimension into 2D
Perform a maximum contrast projection of 3D images along the z-dimension into 2D
Perform a maximum contrast projection of 3D images along the z-dimension into 2D
pipeline for single cell RNA-seq data analysis
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
Post-normalization of total copy numbers
Post-normalization of total copy numbers
Predict gene network using an Ordinary Differential Equation (ODE) based method
Predict gene network using an Ordinary Differential Equation (ODE) based method
Preprocessing of FIA-HRMS data
Preprocessing of FIA-HRMS data
Preprocessing of Illumina Infinium 450K data
Preprocessing of Illumina Infinium 450K data
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays.
Probe Dependent Nearest Neighbours (PDNN) for the affy package
Probe Dependent Nearest Neighbours (PDNN) for the affy package
Probe region expression estimation for RNA-seq data for improved microarray comparability
Probe region expression estimation for RNA-seq data for improved microarray comparability
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Processing and Differential Expression Analysis of Agilent microRNA chips
Processing and Differential Expression Analysis of Agilent microRNA chips
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Provides a GUI for DAPAR
Provides a GUI for DAPAR
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
Quality assessment and low-level analysis for Illumina BeadArray data
Quality assessment and low-level analysis for Illumina BeadArray data
Quality assessment and low-level analysis for Illumina BeadArray data
Quality Control for Single-Cell RNA-seq Data
Quality Control for Single-Cell RNA-seq Data
Quality Control for Single-Cell RNA-seq Data
Quality Control for Single-Cell RNA-seq Data
Quality metrics and data processing methods for NanoString mRNA gene expression data
Quality metrics and data processing methods for NanoString mRNA gene expression data
Quantify and Annotate Short Reads in R
Quantify and Annotate Short Reads in R
Quantitative DNA sequencing for chromosomal aberrations
Quantitative DNA sequencing for chromosomal aberrations
Quantitative DNA sequencing for chromosomal aberrations
Quick Read Quality Control
Quick Read Quality Control
Quick Read Quality Control
RBioinf
RBioinf
Rcpp Integration Surrogate Variable Analysis
Recalibrating Quality Of Nucleotides
Recalibrating Quality Of Nucleotides
Removal of unwanted variation for gene-gene correlations and related analysis.
Remove Unwanted Variation from RNA-Seq Data
Remove Unwanted Variation from RNA-Seq Data
Remove Unwanted Variation from RNA-Seq Data
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
R functions for the normalization of Exiqon miRNA array data
R functions for the normalization of Exiqon miRNA array data
R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
R Investigation of ChIP-chip Oligoarrays
R Investigation of ChIP-chip Oligoarrays
RnBeads
RnBeads
Robust Analysis of MicroArrays
Robust Analysis of MicroArrays
Robust Probabilistic Averaging for probe-level analysis (RPA)
Routines that don't belong to the core flow packages yet.
R package for calling CNV from Illumina 450k methylation microarrays
R package for calling CNV from Illumina 450k methylation microarrays
R package for combining multiple scans
R package for combining multiple scans
RPA: Robust Probabilistic Averaging for probe-level analysis
RPA: Robust Probabilistic Averaging for probe-level analysis
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
Segmentation, normalisation and processing of aCGH data.
Segmentation, normalisation and processing of aCGH data.
Simple tiling array analysis of Affymetrix ChIP-chip data
Simple tiling array analysis of Affymetrix ChIP-chip data
Simplified RNA-Seq Analysis Pipeline
Simplified RNA-Seq Analysis Pipeline
Single-cell analysis toolkit for gene expression data in R
Single-cell analysis toolkit for gene expression data in R
Single-cell analysis toolkit for gene expression data in R
Single Cell Overview of Normalized Expression data
Single Cell Overview of Normalized Expression data
Single Cell Overview of Normalized Expression data
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
SiRNA correction for seed mediated off-target effect
SiRNA correction for seed mediated off-target effect
Smooth quantile normalization
Smooth quantile normalization
Soft clustering of time series gene expression data
Soft clustering of time series gene expression data
Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
Statistical analysis of high-throughput RNAi screens
Statistical analysis of high-throughput RNAi screens
Statistical analysis of peptide microarrays
Statistical analysis of peptide microarrays
Statistical analysis of peptide microarrays
Statistical analysis of sequins
Statistical analysis of sequins
Statistical analysis of sequins
Statistical analysis of Solexa sequencing data
Statistical Analysis of the GeneChip
Statistical Analysis of the GeneChip
Statistics and dIagnostic Graphs for HTS
Statistics and dIagnostic Graphs for HTS
Stepwise normalization functions for cDNA microarrays
Stepwise normalization functions for cDNA microarrays
Subread sequence alignment for R
Subread sequence alignment for R
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Supervised Normalization of Microarrays
Supervised Normalization of Microarrays
Supervised Normalization of Microarrays
Surrogate Variable Analysis
Surrogate Variable Analysis
Surrogate Variable Analysis
SVM2CRM: support vector machine for cis-regulatory elements detections
SVM2CRM: support vector machine for cis-regulatory elements detections
The Cancer Genome Atlas Data Integration
The Cancer Genome Atlas Data Integration
The Cancer Genome Atlas Data Integration
The GASSCO method for correcting for slide-dependent gene-specific dye bias
The GASSCO method for correcting for slide-dependent gene-specific dye bias
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
This package was built to cluster gene expression data using the Gaussian Infinite Mixture Model.
Tools for HELP data analysis
Tools for HELP data analysis
Tools for microbiome analysis
Tools for the Differential Analysis of Proteins Abundance with R
Tools for the Differential Analysis of Proteins Abundance with R
Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level
Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level
Tools to assess and compare miRNA expression estimatation methods
Tools to assess and compare miRNA expression estimatation methods
Transcription Start Site Identification
Transcription Start Site Identification
Transcript mapping with high-density oligonucleotide tiling arrays
Transcript mapping with high-density oligonucleotide tiling arrays
Transform and Filter SWATH Data for Statistical Packages
Transform and Filter SWATH Data for Statistical Packages
Variance stabilization and calibration for microarray data
Variance stabilization and calibration for microarray data
Very simple high level analysis of Affymetrix data
Very simple high level analysis of Affymetrix data
Visualize artificial correlation in microarray data
Visualize artificial correlation in microarray data
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
You Only Lookup One (small part of an otherwise large matrix)