Bioconductor Packages

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

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

Calculate similarity of clusters from different single cell samples using foldchanges

Deep characterization of cancer drugs

Differentially regulated genes from scRNA-seq data

Ensemble of Gene Set Enrichment Analyses

find influential TF and Target based on multi-omics data

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Predicting Targets for Drosophila Intragenic miRNAs

MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

In-silico methods for genetic finemapping in inbred mice

Analysis of Error-Corrected Sequencing Data for Mutation Detection

NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Detection of miRNAs that regulate interacting groups of pathways

Quantile Rank Score

RNA Centric Annotation System

RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Gene regulator enrichment analysis

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

SMTrackR: an R/Bioconductor package for mapping protein binding at individual DNA molecules

Calculates cell type specificity from single cell data

Predicting cell states and their variability in single-cell or spatial omics data

An R package to associate peaks and target genes

R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factors

Tools for the analysis of heterogeneous tissues

A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data

Predict cis-co-accessibility from single-cell chromatin accessibility data

Comprehensive design of CRISPR gRNAs for nucleases and base editors

Exploring curated CRISPR gRNAs via Shiny

Easily install and load the crisprVerse ecosystem for CRISPR gRNA design

Visualization Functions for CRISPR gRNAs

An R package to predict condition-specific enhancers from ChIP-seq data

distinct: a method for differential analyses via hierarchical permutation tests

Gene regulatory network inference from single cell epigenomic data

Companion package to epiregulon with additional plotting, differential and graph functions

Multi-Omics data integration

Inferring miRNA sponge modules in heterogeneous data

Generation of null ranges via bootstrapping or covariate matching

Temporal and Multiplex PageRank for Gene Regulatory Network Analysis

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

R interface to the IGVF Catalog

Statistical analysis of RNA editing sites and hyper-editing regions

Systems biology tool to simulate gene regulatory circuits

Collection and implementation of public transcriptional cancer signatures

spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

Weighting protein-protein interactions