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 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 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

alpine

alternative CDF environments (aka probeset mappings)

Analysis and quantitation of isobarically tagged MSMS proteomics 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-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 single-cell epigenomics datasets with a Shiny App

Analysis tools for Single Molecule Footprinting (SMF) data

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

An Easy Pipeline for NanoString nCounter 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 Variation Detection Method for Whole Exome Sequencing

An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations

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 Bayesian analysis of differential subcellular localisation experiments

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

A package for importing and analyzing data from Roche's Genome Sequencer System

A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

A pipeline for processing drug sensitivity screen data

ArrayAnalysis

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

Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

Assess Differential Gene Expression Experiments with ERCC Controls

Assess Gene Predictions Using Proteomics and Evolutionary Conservation

Assessing array quality on spotted arrays

Assessment of duplication rates in RNA-Seq datasets

ATAC-seq Quality Control

A Tidy Transcriptomics introduction to RNA-Seq analyses

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

Automated analysis of high-throughput qPCR data

Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations

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

Automatic and interactive quality control for flow cytometry data

Base Functions and Classes for Mass Spectrometry and Proteomics

Base package for enabling powerful shiny web displays of Bioconductor objects

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Basic and advanced bioinformatics for RegenerationNEXT

Batch Effects Quality Control Software

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Benchmarks for RNA-seq Quantification Pipelines

Big multivariate data plotted interactively

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

Bioinformatics pipelines based on Rcwl

Brings Seurat to the Tidyverse

Brings SingleCellExperiment to the Tidyverse

Brings SummarizedExperiment to the Tidyverse

Brings transcriptomics to the tidyverse

Building Expression Atlas from RNA-Seq data

Calculate strandness information of a bam file

Cell OrderiNg by FluorEScence Signal

Cell type annotation for unannotated single-cell RNA-Seq data

Cellular DNA Barcode Analysis toolkit

CGH Micro-Array NORmalization

ChIPexoQual

chipseq: A package for analyzing chipseq data

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)

Compare Characteristic Features of Count Data Sets

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

Comparing tumour copy number profiles

Comparison, Benchmarking & QC of Epigenomic Datasets

Comparison between multiple levels of gene expression

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Compute cell-type specific enrichments with high resolution

Convenience package for solving some liftover challenges

CopyKit

Copy-Number Analysis of Large Microarray Data Sets

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

Create genotyping plate maps

Cross omic genetic fingerprinting

Cross-platform consensus analysis of genomic measurements via interlaboratory testing method

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 (USC version)

DegNorm: degradation normalization for RNA-seq data

Detecting hidden batch factors through data adaptive adjustment for biological effects

Detect tissue heterogeneity in expression profiles with gene sets

DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates

Diagnostic Plots to Evaluate the Target Decoy Approach

Differential Abundance Analysis of Label-Free Mass Spectrometry Data

Differential cell-type-specific allelic imbalance

Differential Expression Meta-Analysis

Differential pattern analysis for Ribo-seq data

Discriminant Analysis for Evolutionary Inference

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

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Error correction tool for noisy genotyping by sequencing (GBS) data

Estimate Pairwise Interactions from multidimensional features

Estimates Isoform Specific RPF Footprint Densities

Exploratory Data Analysis and Normalization for RNA-Seq

FARMS - Factor Analysis for Robust Microarray Summarization

Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

FASTQ input and manipulation

FASTQ Quality Control

FFPE Artificial Chimeric Read Filter for NGS data

Find SNV/Indel differences between two bam files with near relationship

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

flowClean

For Visualizing Differential Expression Analysis

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 QC Reports For Alevin Output

Generating Tree Hierarchy Visualizations from Gene Expression Data

Gene set analysis accounting for gene-gene correlations

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

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

Higher-Order Deconvolution Survival Analyses

High-Throughput Sequence Analysis using the Aroma Framework

Hits Selection for Synthetic Lethal RNAi Screen Data

Identifying differential DNA loops from chromatin topology 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 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

Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

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

Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Interaction Based Homogeneity for Evaluating Gene Lists

Interactive Differential Expression AnaLysis

Interactive visualization for Illumina methylation arrays

Interactive Visualization of RNA-seq Data Using a Principal Components Approach

Interactive Workflow for Discovering Rhythmicity in Biological Data

Introduction to Tidy Transcriptomics

IP-seq data analysis and vizualization

Iteratively Adjusted Surrogate Variable Analysis

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Label-free data analysis pipeline for optimal identification and quantitation

Linear Models for Microarray Data

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Load FastqQC reports and other NGS related files

Longitudinal system suitability monitoring and quality control for proteomic experiments

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

Mahalanobis Distance Quality Control for microarrays

Mapping, quantification and variant analysis of sequencing data

massiR: MicroArray Sample Sex Identifier

Maximum rank reproducibility

MBDDiff for processing MBDcap-seq datasets

Mean Alterations Using Discrete Expression

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

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

Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls

MsQuality - Quality metric calculation from Spectra and MsExperiment objects

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

Objective Assessment of Copy-Number Estimates

Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies

Optimized local intensity-dependent normalisation of two-color microarrays

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

Permutation-Based Confidence for Molecular Classification

Phylogenetic Reconstruction and Analysis

Pipeline for single cell multi-omic data pre-processing

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

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

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

Preprocessing, analyzing, and reporting of RNA-seq data

Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models

Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Proteomics Label Free Quantification

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 of LC-MS based metabolomics data

Quality Assessment Tools for Oxford Nanopore MinION data

Quality control and analysis tools for Illumina DNA methylation BeadChip

Quality Control for Single-Cell RNA-seq Data

Quality control for target capture experiments

Quality Control of Normalized Gene Expression Data

Quality Control of Protemics Data

Quality Control Pipeline for ChIP-Seq 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 report for microarray data sets

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

Quantifying Differential Features

Quantifying the accuracy of cellular deconvolution

Quantitative DNA Sequencing for Chromosomal Aberrations

Quick Read Quality Control

Randomize Samples for -omics Profiling

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

Repetitive Element Methylation Prediction

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

R Investigation of ChIP-chip Oligoarrays

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

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

RPA: Robust Probabilistic Averaging for probe-level analysis

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

Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data

Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

SEnsible Step-wise Analysis of DNA MEthylation BeadChips

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

Shiny App for loading multiple FastQC reports

Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering

Shiny-based interactive data-quality exploration for omics data

ShinyÉPICo

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 Overview of Normalized Expression data

Single-Cell RNA-Seq Analysis Utilities

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Single-Cell RNA-Seq Utilities

small RNA-Seq Utilities

Spatial Image Analysis of Tissues

Spatial transcriptome analyses of Nanostring's DSP data in R

Spatial Transcriptomics Analysis

Spike-in calibration for cell-free MeDIP

spsBio: A systemPipeShiny plugin for biological data visualization

Statistical analysis of high-throughput RNAi screens

Statistical Analysis of Molecular Profiles

Statistical Characterization of Post-translational Modifications

Statistics and dIagnostic Graphs for HTS

Suite of Functions for Pooled Crispr Screen QC and Analysis

Supervised Normalization of Microarrays

Systematic quality checks on comparative genomics analyses

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: Workflow Environment for Data Analysis and Report Generation

systemPipeShiny: An Interactive Framework for Workflow Management and Visualization

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

The tidyomics blog

Tidy Transcriptomics for Single-cell RNA Sequencing Analyses

Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Tools for Assessing Clustering

Tools for curating, analyzing, and manipulating biological sequences

Tools for data visualization

Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Tools for Genome Wide Association Studies

Tools for HELP data analysis

Tools for Metabolomics Data

Tools for performing taxonomic assignment.

Tools for qPLEX-RIME data analysis

Tools for quantitative proteomics data analysis

Tools for the Differential Analysis of Proteins Abundance with R

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

Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data

Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation

Very simple high level analysis of Affymetrix data

Visual and interactive quality control of large Illumina DNA Methylation array data sets

Visualization functions for spatial transcriptomics data

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

Working with Illumina Basecalling and Demultiplexing input and output files

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

Biocview "QualityControl"

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