Biocview "QualityControl"

A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data
A "corrective make-up" program for microarray chips
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
A DownStream Chemo-Proteomics Analysis Pipeline
A DownStream Chemo-Proteomics Analysis Pipeline
A DownStream Chemo-Proteomics Analysis Pipeline
Affymetrix expression data quality control and reproducibility analysis
Affymetrix Quality Assessment and Analysis Tool
Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
A flexible and comprehensive software for processing omics data.
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 user interface for MSstatsQC package
A graphical user interface for MSstatsQC package
alpine
alpine
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, 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 Large-Scale Radio-Genomic Data
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.
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
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 Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
A normalization and copy number estimation method for single-cell DNA sequencing
A normalization and copy number estimation method for single-cell DNA sequencing
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
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 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 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 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
ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression
A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
A Software Suite for Shallow Sequencing Copy Number Analysis
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
Assess Gene Predictions Using Proteomics and Evolutionary Conservation
Assess Gene Predictions Using Proteomics and Evolutionary Conservation
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
A tool to calculate and validate primers for Golden Gate Cloning
Augmented functionality for analysis of epigenomic variance
A unifying bioinformatics framework for spatial proteomics
A unifying bioinformatics framework for spatial proteomics
Automated analysis of high-throughput qPCR data
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
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 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
Batch Effects Quality Control Software
bcbio RNA-Seq
bcbio RNA-Seq
bcbio Single-Cell RNA-Seq
bcbio Single-Cell RNA-Seq
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Benchmarks for RNA-seq Quantification Pipelines
Benchmarks for RNA-seq Quantification Pipelines
Big multivariate data plotted interactively
Big multivariate data plotted interactively
Big multivariate data plotted interactively
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Bioinformatics pipelines based on Rcwl
Bioinformatics pipelines based on Rcwl
Calculate strandness information of a bam file
Calculate strandness information of a bam file
Calculate strandness information of a bam file
Cell OrderiNg by FluorEScence Signal
Cell type annotation for unannotated single-cell RNA-Seq data
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
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
Compare Characteristic Features of Count Data Sets
Compare Characteristic Features of Count Data Sets
Comparison between multiple levels of gene expression
Compute cell-type specific enrichments with high resolution
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
Cross omic genetic fingerprinting
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
Data Mining and Analysis of Lipidomics Datasets
Data Mining and Analysis of Lipidomics Datasets
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 (USC version)
DegNorm: degradation normalization for RNA-seq data
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detecting hidden batch factors through data adaptive adjustment for biological effects
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
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
DNA IP-seq data analysis
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 RNA-seq Sample Size Analysis
Empirical RNA-seq Sample Size Analysis
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Estimate Pairwise Interactions from multidimensional features
Exploratory Data Analysis and Normalization for RNA-Seq
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 Methylome-Wide Association Study Pipeline for Enrichment Platforms
FASTQ input and manipulation
FASTQ input and manipulation
FASTQ Quality Control
FASTQ Quality Control
Find SNV/Indel differences between two bam files with near relationship
flowClean
flowClean
For Visualizing Differential Expression Analysis
Functions to conduct quality control analysis in methylation data
Functions to conduct quality control analysis in methylation data
geneChip Analysis Package
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate QC Reports For Alevin Output
Generate QC Reports For Alevin Output
Generating Tree Hierarchy Visualizations from Gene Expression Data
Generating Tree Hierarchy Visualizations from Gene Expression Data
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
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Gimpute: An efficient genetic data processing and imputation pipeline
Graphical user interface for OLIN
GUI for limma Package with Affymetrix Microarrays
GUI for limma Package With Two Color Microarrays
Guitar
GWAS trait-associated SNP enrichment analyses in genomic intervals
Handle Illumina methylation data
Handle Illumina methylation data
High-Throughput Sequence Analysis using the Aroma Framework
Hits Selection for Synthetic Lethal RNAi Screen 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
ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers
Improves Early Build Genome Assemblies using Strand-Seq Data
Improves Early Build Genome Assemblies using Strand-Seq Data
Infrastructure for microfluidic oscillatory washing-based ChIP
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
Interaction Based Homogeneity for Evaluating Gene Lists
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
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 Workflow for Discovering Rhythmicity in Biological Data
Interactive Workflow for Discovering Rhythmicity in Biological Data
IP-seq data analysis and vizualization
IP-seq data analysis and vizualization
Iteratively Adjusted Surrogate Variable Analysis
Iteratively Adjusted Surrogate Variable Analysis
Iteratively Adjusted Surrogate Variable Analysis
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
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
Load FastqQC reports and other NGS related files
Load FastqQC reports and other NGS related files
Load FastqQC reports and other NGS related files
Longitudinal system suitability monitoring and quality control for proteomic experiments
Longitudinal system suitability monitoring and quality control for proteomic experiments
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
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
Methods for Continuous Flow Cytometry
Methods for fitting probe-level models
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
MethyLiution: A QC Pipeline For Methylation Data
Microarray Analysis of Differential Expression
Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
Microbial Assemblage Normalized Transcript Analysis
Microbial Assemblage Normalized Transcript Analysis
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
Multivariate Information Criteria to identify important predictors in high dimensional multivariate regression
Multivariate Information Criteria to identify important predictors in high dimensional multivariate regression
multivariate outlier detection for expression array QA
Murine Palate miRNA Expression Analysis
MWASTools: an integrated pipeline to perform metabolome-wide association studies
Nucleosome positioning package for R
Nucleosome positioning package for R
Nucleosome positioning package for R
Nucleosome positioning package for R
Objective Assessment of Copy-Number Estimates
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
PCA-based gene filtering for Affymetrix arrays
Peak-based selection of high quality cytometry data
Peak Matrix Processing and signal batch correction for metabolomics datasets
Peak Matrix Processing and signal batch correction for metabolomics datasets
Permutation-Based Confidence for Molecular Classification
pipeline for single cell RNA-seq data analysis
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
Precise and Accurate Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis
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
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 Report Generation for affyBatch objects
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 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 target capture experiments
Quality control for target capture experiments
Quality Control Pipeline for ChIP-Seq Data
Quality Control Pipeline for ChIP-Seq Data
Quality Control Pipeline for ChIP-Seq Data
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 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
Quantify and interpret divers of variation in multilevel gene expression experiments
Quantify and interpret divers of variation in multilevel gene expression experiments
Quantifying Differential Features
Quantitative DNA Sequencing for Chromosomal Aberrations
Quantitative DNA Sequencing for Chromosomal Aberrations
Quick Read Quality Control
Quick Read Quality Control
Rapid Integration of Term Annotation and Network resources
Rapid Integration of Term Annotation and Network resources
RBioinf
Recalibrating Quality Of Nucleotides
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
RiboseQC, a Comprehensive Ribo-Seq Analysis Tool
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Ribosome Profiling Quality Control
Ribosome Profiling Quality Control
R Investigation of ChIP-chip Oligoarrays
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNA-Seq Utilities
RNA-Seq Utilities
RnBeads
Robust Analysis of MicroArrays
R package for calling CNV from Illumina 450k methylation microarrays
R Package for Processing High Content Screening data
R Package for Processing High Content Screening data
R Package for Processing High Content Screening data
RPA: Robust Probabilistic Averaging for probe-level analysis
RPA: Robust Probabilistic Averaging for probe-level analysis
sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
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
SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.
Shiny App for loading multiple FastQC reports
ShinyEPICO!
Signal-to-Noise applied to Gene Expression Experiments
Simple tiling array analysis of Affymetrix ChIP-chip data
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 RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single-Cell RNA-Seq Utilities
Single-Cell RNA-Seq Utilities
small RNA-Seq Utilities
Spatial Transcriptomics Analysis
Spatial Transcriptomics Analysis
Statistical analysis of high-throughput RNAi screens
Statistical Analysis of Metabolite Profile
Statistical Analysis of Molecular Profiles
Statistical Analysis of Molecular Profiles
Statistics and dIagnostic Graphs for HTS
Statistics and dIagnostic Graphs for HTS
Subread Sequence Alignment and Counting 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
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 GASSCO method for correcting for slide-dependent gene-specific dye bias
Tools For Analyzing Illumina Infinium DNA Methylation Arrays
Tools For Analyzing Illumina Infinium DNA Methylation Arrays
Tools for curating, analyzing, and manipulating biological sequences
Tools for Diagnostics and Corrections of Batch Effects in Proteomics
Tools for Diagnostics and Corrections of Batch Effects in Proteomics
Tools for Genome Wide Association Studies
Tools for Genome Wide Association Studies
Tools for Genome Wide Association Studies
Tools for HELP data analysis
Tools for performing taxonomic assignment.
Tools for qPLEX-RIME data analysis
Tools for qPLEX-RIME data analysis
Tools for the Differential Analysis of Proteins Abundance with R
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
Tools to assess and compare miRNA expression estimatation methods
Transcriptome-guided quality assessment of m6A-seq data
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
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
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
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