Biocview "QualityControl"

A "corrective make-up" program for microarray chips
A "corrective make-up" program for microarray chips
Affymetrix expression data quality control and reproducibility analysis
Affymetrix expression data quality control and reproducibility analysis
Affymetrix Quality Assessment and Analysis Tool
Affymetrix Quality Assessment and Analysis Tool
Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
A Framework for Quality Control
A Framework for Quality Control
A Framework for Quality Control
A gene-signature ranking method based on sample density in PCA space
A Genetic-Based Assay for the Identification of Cell Lines
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.
alpine
alpine
alpine
alternative CDF environments (aka probeset mappings)
alternative CDF environments (aka probeset mappings)
Analysis and quantitation of isobarically tagged MSMS proteomics data
Analysis and quantitation of isobarically tagged MSMS proteomics data
Analysis and quantitation of isobarically tagged MSMS proteomics data
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis of Agilent Microarray Data [draft]
Analysis of Illumina microarray data [A DRAFT - TRUE]
Analysis of Large Affymetrix Microarray Data Sets
Analysis of Large Affymetrix Microarray Data Sets
Analysis of nucleotide, sequence and quality content on fastq files
Analysis of nucleotide, sequence and quality content on fastq files
Analysis of nucleotide, sequence and quality content on fastq files.
Analysis of nucleotide, sequence and quality content on fastq files.
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
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
An R package for metabolomic data analysis
An R package for proteomics data quality control
An R package for proteomics data quality control
An R package for proteomics data quality control
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 importing and analyzing data from Roche's Genome Sequencer System
A package for importing and analyzing data from Roche's Genome Sequencer System
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assessing array quality on spotted arrays
Assessing array quality on spotted arrays
Assessment of duplication rates in RNA-Seq datasets
Assessment of duplication rates in RNA-Seq datasets
ATAC-seq Quality Control
ATAC-seq Quality Control
ATAC-seq Quality Control
ATAC sequencing Quality Control
A unifying bioinformatics framework for spatial proteomics
A unifying bioinformatics framework for spatial proteomics
A unifying bioinformatics framework for spatial proteomics
Automated analysis of high-throughput qPCR data
Automated analysis of high-throughput qPCR data
Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations
Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations
Automatic and interactive quality control for flow cytometry data
Automatic and interactive quality control for flow cytometry data
Base Functions and Classes for Mass Spectrometry and Proteomics
Base Functions and Classes for Mass Spectrometry and Proteomics
Base Functions and Classes for Mass Spectrometry and Proteomics
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq 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
Benchmarks for RNA-seq Quantification Pipelines
Benchmarks for RNA-seq Quantification Pipelines
Benchmarks for RNA-seq Quantification Pipelines
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Cell OrderiNg by FluorEScence Signal
Cell OrderiNg by FluorEScence Signal
CGH Micro-Array NORmalization
CGH Micro-Array NORmalization
ChIPexoQual
ChIPexoQual
chipseq: A package for analyzing chipseq data
chipseq: A package for analyzing chipseq data
ChIP-Seq Statistical Power
ChIP-Seq Statistical Power
ChIP-Seq Statistical Power
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Compare Characteristic Features of Count Data Sets
Comparison between multiple levels of gene expression
Comparison between multiple levels of gene expression
Convenience package for solving some liftover challenges
Convenience package for solving some liftover challenges
Copy-Number Analysis of Large Microarray Data Sets
Copy-Number Analysis of Large Microarray Data Sets
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
Create genotyping plate maps
Cross omic genetic fingerprinting
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
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detect tissue heterogeneity in expression profiles with gene sets
Detect tissue heterogeneity in expression profiles with gene sets
Detect tissue heterogeneity in expression profiles with gene sets
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
Efficient algorithms for DNA methylation
Efficient compression and analysis of Hi-C Data
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
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
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
FASTQ input and manipulation
FASTQ input and manipulation
Find SNV/Indel differences between two bam files with near relationship
Find SNV/Indel differences between two bam files with near relationship
flowClean
flowClean
flowClean
geneChip Analysis Package
geneChip Analysis Package
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Graphical user interface for OLIN
Graphical user interface for OLIN
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
Guitar
Guitar
GWAS trait-associated SNP enrichment analyses in genomic intervals
GWAS trait-associated SNP enrichment analyses in genomic intervals
Handle Illumina methylation data
Handle Illumina methylation data
Handle Illumina methylation 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
Identifying differential DNA loops from chromatin topology data
Identifying differential DNA loops from chromatin topology data
Identifying differential DNA loops from chromatin topology data
Identify likely duplicate samples from genomic or meta-data
Identify likely duplicate samples from genomic or meta-data
Identify likely duplicate samples from genomic or meta-data
Illumina 450K methylation array spatial analysis methods
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
Improves Early Build Genome Assemblies using Strand-Seq Data
Improves Early Build Genome Assemblies using Strand-Seq Data
Improves Early Build Genome Assemblies using Strand-Seq Data
Interaction Based Homogeneity for Evaluating Gene Lists
Interaction Based Homogeneity for Evaluating Gene Lists
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive visualization for Illumina methylation arrays
Interactive visualization for Illumina methylation arrays
Interactive visualization for Illumina methylation arrays
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
IP-seq data analysis and vizualization
IP-seq data analysis and vizualization
Iteratively Adjusted Surrogate Variable Analysis
Label-free data analysis pipeline for optimal identification and quantitation
Label-free data analysis pipeline for optimal identification and quantitation
Label-free data analysis pipeline for optimal identification and quantitation
Linear Models for Microarray Data
Linear Models for Microarray Data
Linear Models for Microarray Data
Longitudinal system suitability monitoring and quality control for proteomic experiments
Mahalanobis Distance Quality Control for microarrays
Mahalanobis Distance Quality Control for microarrays
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
MBDDiff for processing MBDcap-seq datasets
Measuring the reproducibility of Hi-C data
Measuring the reproducibility of Hi-C data
Measuring the reproducibility of Hi-C data
Measuring the reproducibility of Hi-C data
Methods for Continuous Flow Cytometry
Methods for fitting probe-level models
Methods for fitting probe-level models
Methods for identifying small RNA loci from high-throughput sequencing data
Methods for identifying small RNA loci from high-throughput sequencing data
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
Microarray Analysis of Differential Expression
Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
Microbial Assemblage Normalized Transcript Analysis
Microbial Assemblage Normalized Transcript Analysis
multivariate outlier detection for expression array QA
multivariate outlier detection for expression array QA
Murine Palate miRNA Expression Analysis
Murine Palate miRNA Expression Analysis
MWASTools: an integrated pipeline to perform metabolome-wide association studies
MWASTools: an integrated pipeline to perform metabolome-wide association studies
Objective Assessment of Copy-Number Estimates
Optimized local intensity-dependent normalisation of two-color microarrays
Optimized local intensity-dependent normalisation of two-color microarrays
OSAT: Optimal Sample Assignment Tool
OSAT: Optimal Sample Assignment Tool
Package for enabling powerful shiny web displays of Bioconductor objects
Package for enabling powerful shiny web displays of Bioconductor objects
PCA-based gene filtering for Affymetrix arrays
PCA-based gene filtering for Affymetrix arrays
Permutation-Based Confidence for Molecular Classification
Permutation-Based Confidence for Molecular Classification
pipeline for single cell RNA-seq data analysis
pIR: Estimating Isoelectric Point (pI) of Peptide and Proteins from Amino Acid Sequence.
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
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
QC Report Generation for affyBatch objects
QC Report Generation for affyBatch objects
Quality assessment and control for FFPE microarray expression data
Quality assessment and control for FFPE microarray 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 Assessment Tools for Oxford Nanopore MinION data
Quality Assessment Tools for Oxford Nanopore MinION 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 control for target capture experiments
Quality control for target capture experiments
Quality Control Tool for High-Throughput Sequencing Data
Quality Control Tool for High-Throughput Sequencing Data
Quality Control, Visualization and Processing for High-Throughput Sequencing data
Quality Control, Visualization and Processing for High-Throughput Sequencing 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
Quality metrics for ChIPseq data
Quality metrics for ChIPseq data
Quality metrics report for microarray data sets
Quality metrics report for microarray data sets
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
Rapid Integration of Term Annotation and Network resources
Rapid Integration of Term Annotation and Network resources
Rapid Integration of Term Annotation and Network resources
RBioinf
RBioinf
Recalibrating Quality Of Nucleotides
Recalibrating Quality Of Nucleotides
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
R Investigation of ChIP-chip Oligoarrays
R Investigation of ChIP-chip Oligoarrays
RNA-Seq Utilities
RNA-Seq Utilities
RnBeads
RnBeads
Robust Analysis of MicroArrays
Robust Analysis of MicroArrays
Robust Probabilistic Averaging for probe-level analysis (RPA)
R package for calling CNV from Illumina 450k methylation microarrays
R package for calling CNV from Illumina 450k methylation microarrays
RPA: Robust Probabilistic Averaging for probe-level analysis
RPA: Robust Probabilistic Averaging for probe-level analysis
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
Signal-to-Noise applied to Gene Expression Experiments
Signal-to-Noise applied to Gene Expression Experiments
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-Cell RNA-Seq Utilities
Single-Cell RNA-Seq Utilities
Statistical analysis of high-throughput RNAi screens
Statistical analysis of high-throughput RNAi screens
Statistical Analysis of Metabolite Profile
Statistical Analysis of Metabolite Profile
Statistical Analysis of Metabolite Profile
Statistical analysis of Solexa sequencing data
Statistics and dIagnostic Graphs for HTS
Statistics and dIagnostic Graphs for HTS
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
systemPipeRdata: NGS workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: NGS workflow and report generation environment
TARgeted SEQuencing Experiment Quality Control
TARgeted SEQuencing Experiment Quality Control
The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
The GASSCO method for correcting for slide-dependent gene-specific dye bias
The GASSCO method for correcting for slide-dependent gene-specific dye bias
Tools for curating, analyzing, and manipulating biological sequences
Tools for curating, analyzing, and manipulating biological sequences
Tools for Genome Wide Association Studies
Tools for Genome Wide Association Studies
Tools for HELP data analysis
Tools for HELP data analysis
Tools for performing taxonomic assignment.
Tools for performing taxonomic assignment.
Tools for the Differential Analysis of Proteins Abundance with R
Tools for the Differential Analysis of Proteins Abundance with R
Tools to assess and compare miRNA expression estimatation methods
Tools to assess and compare miRNA expression estimatation methods
Transcriptome-guided quality assessment of methylated RNA immunoprecipitation sequencing data
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Very simple high level analysis of Affymetrix data
Very simple high level analysis of Affymetrix data
Visual and interactive quality control of large Illumina DNA Methylation array data sets
Visual and interactive quality control of large Illumina DNA Methylation array data sets
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
Working with Illumina Basecalling and Demultiplexing input and output files
Working with Illumina Basecalling and Demultiplexing input and output files
Working with Illumina Basecalling and Demultiplexing input and output files
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