Bioconductor Packages

Model higher-order methylation profiles

Computational pipeline for computing probability of modification from structure probing experiment data

Batch Effects Correction with Unknown Subtypes

Batch Effect Correction with Unknow Subtypes for scRNA-seq data

Candidate Driver Analysis

Calculate similarity of clusters from different single cell samples using foldchanges

FEAture SelcTion (FEAST) for Single-cell clustering

FeatSeekR an R package for unsupervised feature selection

GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets

Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Multi Omic Master Regulator Analysis

Bayesian clustering and imputationa of single cell methylomes

A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Predict open reading frames in nucleotide sequences

A package for nonlinear dimension reduction with Isomap and LLE.

RFGeneRank: Cross-validated Stable Predictive Gene Ranking for Transcriptomics

Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Deconvolution of mixed cells from spatial and/or bulk gene expression data

SpectralTAD: Hierarchical TAD detection using spectral clustering

Differential Variability (DV) analysis for single-cell RNA sequencing data. (e.g. Identify Differentially Variable Genes across two experimental conditions)

TADCompare: Identification and characterization of differential TADs

Tensor Decomposition Based Unsupervised Feature Extraction

Advanced package of tensor decomposition based unsupervised feature extraction

XAItest: Enhancing Feature Discovery with eXplainable AI

Feature Extraction for scRNA-seq Dataset Integration

Context-Aware Transcript Quantification from Long Read RNA-Seq data

Signature discovery from omics data

Differential abundance analysis with a right censored covariate in high-dimensional cytometry

consensus Independent Component Analysis

Differential discovery in high-dimensional cytometry via high-resolution clustering

Evaluation of Bioinformatics Metrics

Interactive SummarizedExperiment Explorer

Streamlining the creation of initial states for starting an iSEE instance

iSEE Universe

Iteratively Adjusted Surrogate Variable Analysis

Visualization and evaluation of protein immunogens

Summarize, Analyze and Visualize MAF Files

GWAS Incorporating Networks

Binned Motif Enrichment Analysis and Visualization

multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles

Scoring Personalized Molecular Portraits

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Post-transcriptional network modeling

preciseTAD: A machine learning framework for precise TAD boundary prediction

Quantification of the Tumor Immune contexture from RNA-seq data

Signature-based Clustering for Diagnostic Purposes

RNA editing tools in R