Biocview "GeneRegulation"

A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment

A Functional Approach To Impute Genetically Regulated Expression

AI and ML excursions with Bioconductor and tidymodels

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Analysis of co-regulation and inference of 'dual regulons'

analysis of co-regulatory network motifs and inference of 'dual regulons'.

Analysis of Single-Cell CRISPR Screen Data

Analyze massively parallel reporter assays

Analyze Transcription Factor Enrichment

An integrated analysis package of miRNA and mRNA expression data

annotation of noncoding RNAs and coexpressed genes

A package of creating an algorithm of identifying microRNA-competing endogenous RNA triplets

A shiny user interface for rTRM

Associates DNA Methylation with Matched gene Expression

ATAC-seq Quality Control

A toolkit for APA analysis using RNA-seq data

Basic and advanced bioinformatics for RegenerationNEXT

Basic peak calling on STARR-seq data

Bayesian clustering and imputationa of single cell methylomes

Bayesian modelling of cell-to-cell DNA methylation heterogeneity

Bias-free Footprint Enrichment Test

BIMEGA: BIvariate Methylation and Expression GAussian mixture model

Binding site defintion based on iCLIP data

Bioc2019PanCancerStudy

Biological Network Reconstruction Omnibus

Call wide peaks for sequencing data

ceRNAR: An R Package for Identification and Analysis of ceRNAs-miRNA Triplets

Chromatin Variation Across Regions

CNE Detection and Visualization

co-expression of lincRNAs and protein-coding genes

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

Comparison between multiple levels of gene expression

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

Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

Coordinate Covariation Analysis

CoRegFlux

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

crisprseekplus

Data package for JASPAR 2016

decoupleR: Ensemble of computational methods to infer biological activities from omics data

DeepBlueR

Delineate outstanding genomic zones of differential gene activity

Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

Differential cell-type-specific allelic imbalance

Differential Expressed Windows Based on Negative Binomial Distribution

Differential pattern analysis for Ribo-seq data

DynaMO predicts spatiotemporal binding of transcription factors

Engineering Evaluation by Gene Categorization (eegc)

epiwraps: Wrappers for plotting and dealing with epigenomics data

Estimate Promoter Activity from RNA-Seq data

Estimation of genetic and molecular regulatory networks from high-throughput genomics data

Evolutionary and plasticity analysis of orthologous groups

Exon-Intron Split Analysis (EISA) in R

Exposome and omic data associatin and integration analysis

find influential TF and Target based on multi-omics data

Fit transcriptional regulatory networks using gene expression, priors, machine learning

Functionality Visualization for Motifs

Functions for analyzing SELEX-seq data

Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering

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

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

Generation of null ranges via bootstrapping or covariate matching

Gene Regulatory Network Inference Using Time Series

Gene Set Analysis Using the Outcome of Differential Methylation

Gene Set Regulation (GS-Reg)

Gene Set Regulation Index

Genotype Imputed Gene Set Enrichment Analysis

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

GUIDE-seq analysis pipeline

GUIDE-seq and PEtag-seq analysis pipeline

Identification of enriched motif pairs from chromatin interaction data

Identification of genetic Variants affecting Alternative Splicing

Identification of potential quadruplex forming sequences

Identification of putative mammalian orthologs to given enhancer

Identification of transcriptional regulatory modules from PPI networks

Identify Different Architectures of Sequence Elements

Identify oncogenes and tumor suppressor genes from omics data

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Import, Modify, and Export Motifs with R

Inference of gene regulatory networks from gene expression data

Inference of Genetic Variants Driving Cellular Phenotypes

Inferring miRNA sponge modules in heterogeneous data

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

Integrative analysis of Multi-omics data for Alternative Splicing

Integrative analysis of multi-omics data to infer regulatory networks

Integrative Statistics of alleLe Dependent Expression

Interpretable marker-based single-cell pseudotime using Bayesian parametric models

Irreproducible Discovery Rate for Genomic Interactions Data

Locus overlap analysis for enrichment of genomic ranges

Mapping, quantification and variant analysis of sequencing data

Maximum Likelihood Decay Modeling of RNA Degradation Data

Mean Alterations Using Discrete Expression

Methylation-Based Inference of Regulatory Activity

MethylMix: Identifying methylation driven cancer genes

miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer

Model higher-order methylation profiles

Modeling Network State Transitions from Expression and Regulatory data (MONSTER)

Modeling RNA synthesis, processing and degradation with RNA-seq data

MoPS - Model-based Periodicity Screening

motif matching, comparison, and de novo discovery using the MEME Suite

Obtain total affinity and occupancies for binding site matrices on a given sequence

OmniPath web service client

OmniPath web service client and more

PANDA Algorithm

Pathway RespOnsive GENes for activity inference from gene expression

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

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

Predicting binding site consensus from ranked DNA sequences

Prediction of pri-miRNA Transcription Start Site

Profile score distributions

Promoter identification from large-scale TSS profiling data

Quantifying Differential Features

RcisTarget: Identify transcription factor binding motifs enriched on a gene list

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

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

regutools: an R package for data extraction from RegulonDB

Ribosome Profiling Quality Control

'rifi' analyses data from rifampicin time series created by microarray or RNAseq

R Interface with InterMine-Powered Databases

R package for RIVER (RNA-Informed Variant Effect on Regulation)

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Search and visualize intramolecular triplex-forming sequences in DNA

Single Cell Inference of Regulatory Activity

Software Package for Transcription Factor Binding Site (TFBS) Analysis

Sparse Partial Correlations On Gene Expression

SPIA-PCC: Signaling pathway impact analysis incorporated the change of Pearson correla-tion coefficient between two groups

SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data

StarBioTrek

Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains

Survival analysis using transcriptional networks inferred by the RTN package

Synthetic Expression Data for Gene Regulatory Network Inference

Systems biology tool to simulate gene regulatory circuits

Systems EPigenomics Inference of Regulatory Activity

TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"

The scigenex package (Single-Cell Informative GENe Explorer)

This package classifies putative polyadenylation sites as true or false/internally oligodT primed

Tools for the Efficient Analysis of High-Resolution Genomics Data

Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

Training of logical models from indirect measurements of perturbation experiments

Transcriptional Rewiring

Transcription Factor Enrichment Analysis for ATAC-seq

Transcription factor Inference through Gaussian process Reconstruction of Expression

TSS sequencing data analysis

Unified methods for the inference and analysis of gene regulatory networks

Virtual Inference of Protein-activity by Enriched Regulon analysis

xcore expression regulators inference

Biocview "GeneRegulation"

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