Biocview "GeneRegulation"

A Bioconductor package for identifying novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
A Bioconductor package for identifying novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment
A Functional Approach To Impute Genetically Regulated Expression
A Functional Approach To Impute Genetically Regulated Expression
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
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 co-regulatory network motifs and inference of 'dual regulons'.
analysis of co-regulatory network motifs and inference of 'dual regulons'.
Analyze massively parallel reporter assays
Analyze massively parallel reporter assays
Analyze Transcription Factor Enrichment
Analyze Transcription Factor Enrichment
An integrated analysis package of miRNA and mRNA expression data
An integrated analysis package of miRNA and mRNA expression data
annotation of noncoding RNAs and coexpressed genes
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
ATAC-seq Quality Control
ATAC-seq Quality Control
ATAC-seq Quality Control
A toolkit for APA analysis using RNA-seq data
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 clustering and imputationa of single cell methylomes
Bayesian modelling of cell-to-cell DNA methylation heterogeneity
Bias-free Footprint Enrichment Test
Bias-free Footprint Enrichment Test
BIMEGA: BIvariate Methylation and Expression GAussian mixture model
Bioc2019PanCancerStudy
Biological Network Reconstruction Omnibus
Call wide peaks for sequencing data
Call wide peaks for sequencing data
Call wide peaks for sequencing data
Chromatin Variation Across Regions
Chromatin Variation Across Regions
CNE Detection and Visualization
CNE Detection and Visualization
co-expression of lincRNAs and protein-coding genes
co-expression of lincRNAs and protein-coding genes
CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems
Comparison between multiple levels of gene expression
Computational pipeline for computing probability of modification from structure probing experiment data
Computational pipeline for computing probability of modification from structure probing experiment data
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Coordinate Covariation Analysis
CoRegFlux
CoRegFlux
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
crisprseekplus
crisprseekplus
CTDPathSim: Cell line-tumor deconvoluted pathway-based similarity in the context of precision medicine in cancer
Data package for JASPAR 2016
DeepBlueR
DeepBlueR
DeepBlueR
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
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)
Engineering Evaluation by Gene Categorization (eegc)
Estimate Promoter Activity from RNA-Seq data
Estimate Promoter Activity from RNA-Seq data
Estimation of genetic and molecular regulatory networks from high-throughput genomics 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
Exon-Intron Split Analysis (EISA) in R
Exposome and omic data associatin and integration analysis
Exposome and omic data associatin and integration analysis
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
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
Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
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
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
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Gene Regulatory Network Inference Using Time Series
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
Gene Set Regulation Index
Genotype Imputed Gene Set Enrichment Analysis
Genotype Imputed Gene Set Enrichment Analysis
GUIDE-seq analysis pipeline
GUIDE-seq analysis pipeline
Identification of genetic Variants affecting Alternative Splicing
Identification of potential quadruplex forming sequences
Identification of transcriptional regulatory modules from PPI networks
Identify Different Architectures of Sequence Elements
Identify oncogenes and tumor suppressor genes from omics data
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
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 miRNA sponge modules in heterogeneous data
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
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 for Alternative Splicing
Integrative Statistics of alleLe Dependent Expression
Integrative Statistics of alleLe Dependent Expression
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
Irreproducible Discovery Rate for Genomic Interactions Data
Irreproducible Discovery Rate for Genomic Interactions Data
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Mapping, quantification and variant analysis of sequencing data
Maximum Likelihood Decay Modeling of RNA Degradation Data
Maximum Likelihood Decay Modeling of RNA Degradation Data
Mean Alterations Using Discrete Expression
Methylation-Based Inference of Regulatory Activity
Methylation-Based Inference of Regulatory Activity
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer
Model higher-order methylation profiles
Model higher-order methylation profiles
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
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
motif matching, comparison, and de novo discovery using the MEME Suite
Obtain total affinity and occupancies for binding site matrices on a given sequence
Obtain total affinity and occupancies for binding site matrices on a given sequence
OmniPath web service client
OmniPath web service client and more
Package to decouple gene sets from statistics
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
Pathway RespOnsive GENes for activity inference from gene expression
Pathway RespOnsive GENes for activity inference from gene expression
Precict cis-co-accessibility from single-cell chromatin accessibility data
Precict cis-co-accessibility from single-cell chromatin accessibility data
Precict cis-co-accessibility from single-cell chromatin accessibility data
Predicting binding site consensus from ranked DNA sequences
Prediction of pri-miRNA Transcription Start Site
Prediction of pri-miRNA Transcription Start Site
Profile score distributions
Promoter identification from large-scale TSS profiling data
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
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
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
Ribosome Profiling Quality Control
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
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
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
Search and visualize intramolecular triplex-forming sequences in DNA
Single Cell Inference of Regulatory Activity
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Sparse Partial Correlations On Gene Expression
Sparse Partial Correlations On Gene Expression
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
SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
StarBioTrek
StarBioTrek
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
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 biology tool to simulate gene regulatory circuits
Systems biology tool to simulate gene regulatory circuits
Systems biology tool to simulate gene regulatory circuits
Systems EPigenomics Inference of Regulatory Activity
Systems EPigenomics Inference of Regulatory Activity
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
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 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
Training of logical models from indirect measurements of perturbation experiments
Transcriptional Rewiring
Transcription factor Inference through Gaussian process Reconstruction of Expression
Transcription factor Inference through Gaussian process Reconstruction of Expression
TSS sequencing data analysis
Virtual Inference of Protein-activity by Enriched Regulon analysis
Virtual Inference of Protein-activity by Enriched Regulon analysis