Bioconductor Packages

ATAC-seq Quality Control

visualization and annotation of isotopic enrichment patterns of peptides and metabolites with stable isotope labeling from proteomics and metabolomics

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

Assess Gene Predictions Using Proteomics and Evolutionary Conservation

High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batch-Effect Reduction Trees (BERT)

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

Batch Effects Quality Control Software

Identify Batch-Biased Spatially Variable Genes

A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

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

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

Cellular DNA Barcode Analysis toolkit

Quality metrics for ChIPseq data

ChIPexoQual

Analysis of single-cell epigenomics datasets with a Shiny App

Detect and Correct Genomic DNA Contamination in RNA-seq Data

Automated detection tool for spillover errors

Queries the Human Cell Atlas

Low Dimensions projection of cytometry samples

Automation and visualization of flow cytometry data analysis pipelines

GUI's for visualization of flow cytometry data analysis pipelines

Tools for the Differential Analysis of Proteins Abundance with R

Tools for curating, analyzing, and manipulating biological sequences

Differential Expression Meta-Analysis

Methylation array and sequencing spatial analysis methods

Convenient functions to streamline your single cell data analysis workflow

DegNorm: degradation normalization for RNA-seq data

Interactive Workflow for Discovering Rhythmicity in Biological Data

A DownStream Chemo-Proteomics Analysis Pipeline

Estimating Absolute Abundance from Microbial Spike-in Controls

Exploratory Data Analysis and Normalization for RNA-Seq

Quality control and analysis tools for Illumina DNA methylation BeadChip

Empirical RNA-seq Sample Size Analysis

Comparison, Benchmarking & QC of Epigenomic Datasets

FFPE Artificial Chimeric Read Filter for NGS data

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

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

Tools for Genome Wide Association Studies

R Package for Processing High Content Screening data

Population-level Representation on scRNA-Seq data

Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

Guitar

Tools for HELP data analysis

Automated analysis of high-throughput qPCR data

Quality Assessment Tools for Oxford Nanopore MinION data

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

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

CGH Micro-Array NORmalization

Evaluation and correction of batch effects in microbiome data-sets

Plots of Multi Dimensional Scaling (MDS) results