Biocview "Preprocessing"

A "corrective make-up" program for microarray chips

A correlation-based method for quality filtering of single-cell RNAseq data

Adaptive Dropout Imputer (ADImpute)

Adaptive Robust Regression normalization for Illumina methylation data

Adjust for positional and batch effects using ComBat

A DownStream Chemo-Proteomics Analysis Pipeline

A fast scatterplot smoother suitable for microarray normalization

Affymetrix-based RMA Processing Using Fixed Parameters

Affymetrix Quality Assessment and Analysis Tool

A Framework to Combine, Analize and Interpret CNVs Calling Results

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

ALS for the Automatic Chemical Exploration of mixtures

alternative CDF environments (aka probeset mappings)

A model for network-based prioritisation of genes

Analysis and Visualisation of the Human Phenotype Ontology

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 Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Analysis of cell-based screens - revised version of cellHTS

Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)

Analysis of high-throughput microscopy-based screens

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 single-cell epigenomics datasets with a Shiny App

Analysis of Transposable Elements

Analyte Explorer

Analyze and correct probe positional bias in microarray data due to RNA degradation

Analyze Illumina Infinium DNA methylation arrays

An Easy-to-use Systematic pipeline for ATACseq data analysis

An Interactive Consensus Clustering Framework for Multi-platform Data Analysis

An R Object-oriented Microarray Analysis package

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 creation of complex genomic profile plots

An R package of Data Importing, Processing and Analysis for Opera High Content Screening System

An R Wrapper for Bowtie2 and AdapterRemoval

An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).

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 clinical proteomic profiling data analysis

A pipeline for processing drug sensitivity screen data

ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

A Software Suite for Shallow Sequencing Copy Number Analysis

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 Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms

A tool for unsupervised projection of single cell RNA-seq data

a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

Augmented functionality for analysis of epigenomic variance

Automated Affymetrix Array Analysis Preprocessing Package

Automated analysis of high-throughput qPCR data

Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis

Automated spectraL Processing System for NMR

A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Background Adjustment Using Sequence Information

Bandwise normalization and batch correction of Hi-C data

Basic graphic utilities for visualization of genomic data.

Batch Effects Quality Control Software

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Benchmark of differential abundance methods on microbiome data

Bias Awared Peak Calling and Quantification for MeRIP-Seq

Big multivariate data plotted interactively

Binomial test for Hi-C data analysis

Bioinformatics pipelines based on Rcwl

Biological Network Reconstruction Omnibus

Building Expression Atlas from RNA-Seq data

Calibration model for estimating absolute expression levels from microarray data

Calling aberrations for array CGH tumor profiles.

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

CDF Environment Maker

Cellular DNA Barcode Analysis toolkit

CGH Micro-Array NORmalization

C++ infrastructure for representing and interacting with the gated cytometry data

Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Clustering of MS2 Spectra for Metabolite Identification

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Compare Patient Samples to Cell Line Models Using Molecular Data and Weighted Similarity

Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

Compute cell-type specific enrichments with high resolution

Conditional quantile normalization

Connect high throughput Array data from different platforms

Convenience package for solving some liftover challenges

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 information from ChIP_seq using off-target reads 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

Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments

Correction of batch effects in DNA methylation data

Correspondence Analysis for Single Cell Data

Count summarization and normalization for RNA-Seq data

Cross Platform Meta-Analysis of Microarray Data

Cytometry dATa anALYSis Tools

Data-driven normalization strategies for high-throughput qPCR data.

Data normalization by matrix raking

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

DeepBlueR

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

Detecting hidden batch factors through data adaptive adjustment for biological effects

Detection of focal aberrations in DNA copy number data

Differential Analyis of Hi-C Data

Differential Analysis of Hi-C Data

DNA IP-seq data analysis

Effective mobility scale transformation of CE-MS(/MS) data

Efficient algorithms for DNA methylation

Efficient compression and analysis of Hi-C Data

Empirical Bayes estimate of block diagonal covariance matrices

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

EpiMix: an integrative tool for the population-level analysis of DNA methylation

Estimate Pairwise Interactions from multidimensional features

Estimate Promoter Activity from RNA-Seq data

EWCE for Multiple Gene Lists

Excluding host reads from xenograft sequencing data

Exploratory analysis for two-color spotted microarray data

Exploratory Data Analysis and Normalization for RNA-Seq

FARMS - Factor Analysis for Robust Microarray Summarization

Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Fast treatment of MACSQuantify FACS data

FFPE Artificial Chimeric Read Filter for NGS data

Filter replicated high-throughput transcriptome sequencing data

Finding differentially expressed unannotated genomic regions from RNA-seq data

Flexible, isoform-level differential expression analysis

Flexible, probabilistic metrics for quality control of scRNA-seq data

Frozen RMA and Barcode

Frozen RMA Tools

Functions to conduct quality control analysis in methylation data

Functions to handle cDNA microarray data, including several methods of data analysis

Functions to process LM-PCR reads from 454/Illumina data

Functions used to preprocess datasets stored in BioDataome

Gaussian Process Ranking and Estimation of Gene Expression time-series

geneChip Analysis Package

Gene network reconstruction

Gene set analysis accounting for gene-gene correlations

Gene set analysis following differential expression using linear (mixed) modeling with dream

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.

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

Graphical User Interface for IsoCorrectoR

Graphical user interface for OLIN

Graphics Toolbox for Assessment of Affymetrix Expression Measures

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

GUI for limma Package with Affymetrix Microarrays

GUI for limma Package With Two Color Microarrays

Handle Illumina methylation data

Heatmaps of Stack Profiles from Epigenetic Signals

Hierarchical Gating Pipeline for flow cytometry data

High-Throughput Sequence Analysis using the Aroma Framework

Hits Selection for Synthetic Lethal RNAi Screen Data

HIV Annotation

Identification of CTC in Blood Streams

Identify Differentially Expressed Genes from RNA-seq data

Identifying differential DNA loops from chromatin topology data

Illumina 450 methylation array normalization and metrics

Illumina DNA methylation array normalization and metrics

Illumina methylation array analysis for large experiments

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay"

Import and summarize transcript-level estimates for transcript- and gene-level analysis

Importing a tRNAscan-SE result file as GRanges object

Infrastructure for representing and interacting with gated and ungated cytometry data sets.

In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data

integrated Bayesian Modeling of eQTL data

Interactive Cytometry Gating in R

Interactive visualization for Illumina methylation arrays

Interspecies gene mapping

IP-seq data analysis and vizualization

Iteratively Adjusted Surrogate Variable Analysis

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

LC/MS Metabolomics Data Processing Utilities

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 Models for Microarray Data

LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays

LVS normalization for Agilent miRNA data

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

Manipulation of Codelink microarray data

Mapping, quantification and variant analysis of sequencing data

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

MBCB (Model-based Background Correction for Beadarray)

Mean/Median-balanced quantile normalization

megadepth: BigWig and BAM related utilities

MetaCyto: A package for meta-analysis of cytometry data

Methods for Affymetrix Oligonucleotide Arrays

Methods for fitting probe-level models

Methylation array and sequencing spatial analysis methods

Methylation Enriched LOci Normalization (MELON) for genome-wide DNA methylation experiments

MethyLiution: A QC Pipeline For Methylation Data

MiChip Parsing and Summarizing Functions

Microarray Analysis of Differential Expression

Microarray Analysis tool

Microarray and RNA-seq Processing for ImmuneSpace

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

MRS Data Preprocessing and Normalisation

Multi-Scale Target Explorer

Multivariate Information Criteria to identify important predictors in high dimensional multivariate regression

Munich ChronoType Questionnaire Tools

Murine Palate miRNA Expression Analysis

Muscle Epigenetic Age Test

Network smoothing for scRNAseq

NEUral network-based single-Cell Annotation tool

Non-detects in qPCR data

Normalization and difference calling in ChIP-seq data

Normalization and reporting of Illumina SNP bead arrays

Normalization of array CGH data with imbalanced aberrations.

Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit

Optimized local intensity-dependent normalisation of two-color microarrays

Out-of-core statistical computing and signal processing

Package analyse 4C sequencing data

Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data

Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays

Peak-based selection of high quality cytometry data

Perform a maximum contrast projection of 3D images along the z-dimension into 2D

Pipeline for single cell multi-omic data pre-processing

pipeline for single cell RNA-seq data analysis

PKG_TITLE

Platform for integrative analysis of omics data

Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections

Post-normalization of total copy numbers

Precise and Accurate Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis

Predict gene network using an Ordinary Differential Equation (ODE) based method

Prediction of pri-miRNA Transcription Start Site

Pre-process 1H-NMR FID signals

Preprocessing, analyzing, and reporting of RNA-seq data

Preprocessing and Analysis of Deep Mutational Scanning Data

Preprocessing of FIA-HRMS data

Preprocessing of Illumina Infinium 450K data

Preprocessing of spectra data from high resolution mass spectrometry

Pre-processing PTR-TOF-MS Data

Preprocessing tools for oligonucleotide arrays

Preprocessing tools for oligonucleotide arrays.

Probe Dependent Nearest Neighbours (PDNN) for the affy package

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 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)

Protein Micro Array Data Management and Interactive Visualization

Proteomics Label Free Quantification

Provides a GUI for DAPAR

QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data

Quality assessment and low-level analysis for Illumina BeadArray data

Quality control and analysis tools for Illumina DNA methylation BeadChip

Quality Control for Single-Cell RNA-seq Data

Quality metrics and data processing methods for NanoString mRNA gene expression data

Quantification and Visualization of Variations of Splicing in Population

Quantification and Visulization of Variations of Splicing in Population

Quantify and Annotate Short Reads in R

Quantify and interpret divers of variation in multilevel gene expression experiments

Quantify and interpret drivers of variation in multilevel gene expression experiments

Quantitative DNA Sequencing for Chromosomal Aberrations

Quantitative Metabolomics Data Processing Tools

Quick Read Quality Control

Random Rotation Methods for High Dimensional Data with Batch Structure

RBioinf

Rcpp Integration Surrogate Variable Analysis

Recalibrating Quality Of Nucleotides

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

Removal of unwanted variation for gene-gene correlations and related analysis.

Remove Unwanted Variation from RNA-Seq Data

Repetitive Element Methylation Prediction

Reusable and reproducible Data Management

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 Investigation of ChIP-chip Oligoarrays

RnBeads

Robust Analysis of MicroArrays

Robust outlier identification for DNA methylation data

Robust statistical inference for quantitative LC-MS proteomics

Routines that don't belong to the core flow packages yet.

R package for calling CNV from Illumina 450k methylation microarrays

R package for combining multiple scans

R Package for Processing High Content Screening data

RPA: Robust Probabilistic Averaging for probe-level analysis

samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation

sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Scalable identification of spatially variable genes in spatially-resolved transcriptomics data

scDblFinder

Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

scRecover for imputation of single-cell RNA-seq data

Segmentation, normalisation and processing of aCGH data

SEnsible Step-wise Analysis of DNA MEthylation BeadChips

SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

ShinyÉPICo

Simple tiling array analysis of Affymetrix ChIP-chip data

Simplified RNA-Seq Analysis Pipeline

SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

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 RNA-Seq Analysis Utilities

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)

SiRNA correction for seed mediated off-target effect

Smooth quantile normalization

Soft clustering of time series gene expression data

Spatial and intensity based normalization of cDNA microarray data based on robust neural nets

Spatial Transcriptomics Analysis

Spike-in calibration for cell-free MeDIP

SpotClean adjusts for spot swapping in spatial transcriptomics data

Standardise summary statistics from GWAS

Statistical analysis of high-throughput RNAi screens

Statistical Analysis of Molecular Profiles

Statistical analysis of peptide microarrays

Statistical analysis of sequins

Statistical Analysis of the GeneChip

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Statistics and dIagnostic Graphs for HTS

Stepwise normalization functions for cDNA microarrays

Suite of Functions for Pooled Crispr Screen QC and Analysis

Supervised Normalization of Microarrays

Surrogate Variable Analysis

Survival analysis for gene signatures

SVM2CRM: support vector machine for cis-regulatory elements detections

SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures

taxFun

TCGA utility functions for data management

The Cancer Genome Atlas Data Integration

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

This package was built to cluster gene expression data using the Gaussian Infinite Mixture Model.

Tidy Meta Profiles using Bioconductor and the Tidyverse

Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Tools for Assessing Clustering

Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Tools for HELP data analysis

Tools for microbiome analysis

Tools for Omics Data Analysis

Tools for qPLEX-RIME data analysis

Tools for quantitative proteomics data analysis

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 to assess and compare miRNA expression estimatation methods

Tools to Process the Munich ChronoType Questionnaire (MCTQ)

Training of logical models from indirect measurements of perturbation experiments

Transcript abundance linear modeling from compressed coverage information

Transcription Start Site Identification

Transcript mapping with high-density oligonucleotide tiling arrays

Transcriptomic Ovarian Cancer Datasets

Transcript Quantification Import with Automatic Metadata

Transform and Filter SWATH Data for Statistical Packages

Translational control assessment from ribosome footprint and total RNA libraries

TSS sequencing data analysis

UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Unified Statistical Modeling of Omics Data

User-friendly Workflow for Pre-processing and Statistical Analysis of Mass Spectrometry Data

Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation

Variance stabilization and calibration for microarray data

Variance Stabilizing Transformation for Gamma-Poisson Models

Very simple high level analysis of Affymetrix data

Visualize artificial correlation in microarray data

Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip

Viz tool for xcms peak picking parameter optimisation

What the Package Does (One Line, Title Case)

YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

You Only Lookup One (small part of an otherwise large matrix)

Biocview "Preprocessing"

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