Biocview "GeneRegulation"

Analysis of 4sU-seq and RNA-seq time-course data
Analysis of 4sU-seq and RNA-seq time-course data
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'.
Analysis of co-regulatory network motifs and inference of 'dual regulons'
An integrated analysis package of miRNA and mRNA expression data
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 shiny user interface for rTRM
A shiny user interface for rTRM
ATAC-seq Quality Control
ATAC-seq Quality Control
ATAC-seq Quality Control
ATAC sequencing Quality Control
Basic peak calling on STARR-seq data
Basic peak calling on STARR-seq data
BIMEGA: BIvariate Methylation and Expression GAussian mixture model
Call wide peaks for sequencing data
Call wide peaks for sequencing data
Call wide peaks for sequencing data
Chromatin Variation Across Regions
CNE Detection and Visualization
CNE Detection and Visualization
CNE Detection and Visualization
co-expression of lincRNAs and protein-coding genes
co-expression of lincRNAs and protein-coding genes
co-expression of lincRNAs and protein-coding genes
Comparison between multiple levels of gene expression
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
Computational pipeline for computing probability of modification from structure probing experiment data
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
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
crisprseekplus
crisprseekplus
crisprseekplus
Data package for JASPAR 2016
DeepBlueR
DeepBlueR
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
DynaMO predicts spatiotemporal binding of transcription factors
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
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 based on orthologous groups distribution
Evolutionary and plasticity analysis based on orthologous groups distribution
Exposome and omic data associatin and integration
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Functions for analyzing SELEX-seq data
Functions for analyzing SELEX-seq data
Gene Regulatory Network Inference Using Time Series
Gene Regulatory Network Inference Using Time Series
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
Gene Set Regulation Index
Gene Set Regulation Index
GUIDE-seq analysis pipeline
GUIDE-seq analysis pipeline
Identification of genetic Variants affecting Alternative Splicing
Identification of genetic Variants affecting Alternative Splicing
Identification of Novel alternative PolyAdenylation Sites (PAS)
Identification of Novel alternative PolyAdenylation Sites (PAS)
Identification of potential quadruplex forming sequences
Identification of potential quadruplex forming sequences
Identification of transcriptional regulatory modules from PPI networks
Identification of transcriptional regulatory modules from PPI networks
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
Import, modify, and export motif files with R
Inference of Genetic Variants Driving Cellular Phenotypes
Inference of Genetic Variants Driving Cellular Phenotypes
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Integrative analysis of Multi-omics data for Alternative Splicing
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
Location overlap analysis for enrichment of genomic ranges
Location overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Methylation-Based Inference of Regulatory Activity
Methylation regulation network inference with Conditional Mutual information based PC-algorithem
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
Model higher-order methylation profiles
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)
MoPS - Model-based Periodicity Screening
MoPS - Model-based Periodicity Screening
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
Obtain total affinity and occupancies for binding site matrices on a given sequence
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
Predicting binding site consensus from ranked DNA sequences
Predicting binding site consensus from ranked DNA sequences
Profile score distributions
Profile score distributions
Promoter identification from large-scale TSS profiling data
Promoter identification from large-scale TSS profiling data
Promoter identification from large-scale TSS profiling data
RcisTarget: Identify transcription factor binding motifs enriched on a gene list
Reconstruction of transcriptional networks and analysis of master regulators
Reconstruction of transcriptional networks and analysis of master regulators
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)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
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
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
Search and visualize intramolecular triplex-forming sequences in DNA
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Software Package for Transcription Factor Binding Site (TFBS) Analysis
SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
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
StarTrek
Subread sequence alignment for R
Subread sequence alignment for R
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
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
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"
"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
This package classifies putative polyadenylation sites as true or false/internally oligodT primed
Transcription factor Inference through Gaussian process Reconstruction of Expression
Transcription factor Inference through Gaussian process Reconstruction of Expression
Virtual Inference of Protein-activity by Enriched Regulon analysis
Virtual Inference of Protein-activity by Enriched Regulon analysis
Virtual Inference of Protein-activity by Enriched Regulon analysis