bioconductor.org "GeneRegulation" keyword
View the packages on the bioconductor.org package registry that are tagged with the "GeneRegulation" keyword.
GIGSEA 1.28.0
Genotype Imputed Gene Set Enrichment Analysis6 versions - Latest release: about 1 month ago - 11 thousand downloads total - 1 maintainer
Top 2.4% on bioconductor.org
6 versions - Latest release: about 1 month ago - 2 dependent packages - 299 thousand downloads total - 1 maintainer
DiffBind 3.20.0
Differential Binding Analysis of ChIP-Seq Peak Data6 versions - Latest release: about 1 month ago - 2 dependent packages - 299 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
8 versions - Latest release: 2 months ago - 14 dependent packages - 411 thousand downloads total - 2 maintainers
Rsubread 2.24.0
Mapping, quantification and variant analysis of sequencing data8 versions - Latest release: 2 months ago - 14 dependent packages - 411 thousand downloads total - 2 maintainers
IVAS 2.30.0
Identification of genetic Variants affecting Alternative Splicing6 versions - Latest release: about 1 month ago - 1 dependent package - 21.2 thousand downloads total - 1 maintainer
GUIDEseq 1.40.0
GUIDE-seq and PEtag-seq analysis pipeline6 versions - Latest release: about 1 month ago - 1 dependent package - 21.8 thousand downloads total - 1 maintainer
Melissa 1.25.0
Bayesian clustering and imputationa of single cell methylomes6 versions - Latest release: about 1 month ago - 10.7 thousand downloads total - 1 maintainer
cicero 1.28.0
Predict cis-co-accessibility from single-cell chromatin accessibility data6 versions - Latest release: about 1 month ago - 38 thousand downloads total - 1 maintainer
epiregulon.extra 1.6.0
Companion package to epiregulon with additional plotting, differential and graph functions7 versions - Latest release: about 2 months ago - 4.87 thousand downloads total - 0 stars on GitHub - 1 maintainer
epidecodeR 1.18.0
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation6 versions - Latest release: 2 months ago - 8.09 thousand downloads total - 3 stars on GitHub - 1 maintainer
BiFET 1.30.0
Bias-free Footprint Enrichment Test6 versions - Latest release: about 1 month ago - 16.6 thousand downloads total - 1 maintainer
MoonlightR 1.36.0
Identify oncogenes and tumor suppressor genes from omics data6 versions - Latest release: about 1 month ago - 18.4 thousand downloads total - 17 stars on GitHub - 1 maintainer
FindIT2 1.16.0
find influential TF and Target based on multi-omics data6 versions - Latest release: about 1 month ago - 8.27 thousand downloads total - 6 stars on GitHub - 1 maintainer
scGraphVerse 1.0.0
scGraphVerse: A Gene Network Analysis Package1 version - Latest release: 2 months ago - 412 downloads total - 1 stars on GitHub - 1 maintainer
SPICEY 1.0.0
Calculates cell type specificity from single cell data1 version - Latest release: 2 months ago - 565 downloads total - 0 stars on GitHub - 1 maintainer
scMET 1.12.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity6 versions - Latest release: about 1 month ago - 6.72 thousand downloads total - 18 stars on GitHub - 1 maintainer
idr2d 1.24.0
Irreproducible Discovery Rate for Genomic Interactions Data7 versions - Latest release: about 1 month ago - 11.5 thousand downloads total - 1 maintainer
sarks 1.22.0
Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains6 versions - Latest release: about 1 month ago - 9.19 thousand downloads total - 1 maintainer
CAGEfightR 1.30.0
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor6 versions - Latest release: about 1 month ago - 1 dependent package - 29.4 thousand downloads total - 9 stars on GitHub - 1 maintainer
COCOA 2.24.0
Coordinate Covariation Analysis6 versions - Latest release: about 1 month ago - 14.2 thousand downloads total - 1 maintainer
GSRI 2.58.0
Gene Set Regulation Index6 versions - Latest release: about 1 month ago - 33 thousand downloads total - 1 maintainer
BPRMeth 1.35.0
Model higher-order methylation profiles6 versions - Latest release: about 1 month ago - 1 dependent package - 20.6 thousand downloads total - 1 maintainer
pandaR 1.42.0
PANDA Algorithm6 versions - Latest release: about 1 month ago - 1 dependent package - 24.3 thousand downloads total - 2 maintainers
Top 7.7% on bioconductor.org
6 versions - Latest release: about 2 months ago - 46.4 thousand downloads total - 2 maintainers
GDCRNATools 1.30.0
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data i...6 versions - Latest release: about 2 months ago - 46.4 thousand downloads total - 2 maintainers
Cogito 1.16.0
Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic...6 versions - Latest release: about 1 month ago - 7.61 thousand downloads total - 1 maintainer
memes 1.18.0
motif matching, comparison, and de novo discovery using the MEME Suite6 versions - Latest release: about 1 month ago - 21.4 thousand downloads total - 43 stars on GitHub - 1 maintainer
BUMHMM 1.34.0
Computational pipeline for computing probability of modification from structure probing experimen...6 versions - Latest release: about 1 month ago - 16.2 thousand downloads total - 1 maintainer
BasicSTARRseq 1.38.0
Basic peak calling on STARR-seq data6 versions - Latest release: about 1 month ago - 19.4 thousand downloads total - 1 maintainer
geneplast 1.36.0
Evolutionary and plasticity analysis of orthologous groups6 versions - Latest release: about 1 month ago - 1 dependent package - 18.4 thousand downloads total - 1 maintainer
TENET 1.2.0
R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key...3 versions - Latest release: about 1 month ago - 2.08 thousand downloads total - 1 stars on GitHub - 1 maintainer
triplex 1.50.0
Search and visualize intramolecular triplex-forming sequences in DNA6 versions - Latest release: about 1 month ago - 27.3 thousand downloads total - 1 maintainer
DEWSeq 1.24.0
Differential Expressed Windows Based on Negative Binomial Distribution6 versions - Latest release: about 2 months ago - 11.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
7 versions - Latest release: about 1 month ago - 124 thousand downloads total - 1 maintainer
RcisTarget 1.29.0
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic re...7 versions - Latest release: about 1 month ago - 124 thousand downloads total - 1 maintainer
regutools 1.22.0
regutools: an R package for data extraction from RegulonDB6 versions - Latest release: about 1 month ago - 10.4 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
6 versions - Latest release: about 1 month ago - 1 dependent package - 340 thousand downloads total - 4 stars on GitHub - 1 maintainer
CNEr 1.46.0
CNE Detection and Visualization6 versions - Latest release: about 1 month ago - 1 dependent package - 340 thousand downloads total - 4 stars on GitHub - 1 maintainer
SELEX 1.42.0
Functions for analyzing SELEX-seq data6 versions - Latest release: about 1 month ago - 19.5 thousand downloads total - 1 maintainer
spatzie 1.15.1
Identification of enriched motif pairs from chromatin interaction data6 versions - Latest release: about 1 month ago - 6.89 thousand downloads total - 1 maintainer
RiboDiPA 1.18.0
Differential pattern analysis for Ribo-seq data6 versions - Latest release: about 1 month ago - 8.98 thousand downloads total - 1 maintainer
ATACseqTFEA 1.12.0
Transcription Factor Enrichment Analysis for ATAC-seq6 versions - Latest release: about 2 months ago - 7.02 thousand downloads total - 1 stars on GitHub - 1 maintainer
BindingSiteFinder 2.8.0
Binding site defintion based on iCLIP data6 versions - Latest release: about 1 month ago - 8.43 thousand downloads total - 3 stars on GitHub - 1 maintainer
tRanslatome 1.48.0
Comparison between multiple levels of gene expression6 versions - Latest release: about 1 month ago - 27.8 thousand downloads total - 2 maintainers
IMAS 1.33.1
Integrative analysis of Multi-omics data for Alternative Splicing6 versions - Latest release: about 1 month ago - 15.4 thousand downloads total - 1 maintainer
RTNsurvival 1.34.0
Survival analysis using transcriptional networks inferred by the RTN package6 versions - Latest release: about 1 month ago - 15.1 thousand downloads total - 2 maintainers
Top 7.4% on bioconductor.org
6 versions - Latest release: about 1 month ago - 50 thousand downloads total - 1 maintainer
ELMER 2.33.1
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes6 versions - Latest release: about 1 month ago - 50 thousand downloads total - 1 maintainer
profileScoreDist 1.38.0
Profile score distributions6 versions - Latest release: about 1 month ago - 14.7 thousand downloads total - 1 maintainer
GenomicOZone 1.24.0
Delineate outstanding genomic zones of differential gene activity6 versions - Latest release: about 1 month ago - 10.9 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
6 versions - Latest release: about 1 month ago - 7 dependent packages - 97.7 thousand downloads total - 1 maintainer
viper 1.44.0
Virtual Inference of Protein-activity by Enriched Regulon analysis6 versions - Latest release: about 1 month ago - 7 dependent packages - 97.7 thousand downloads total - 1 maintainer
rTRMui 1.48.0
A shiny user interface for rTRM6 versions - Latest release: about 1 month ago - 23.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
OmnipathR 3.18.3
OmniPath web service client and more10 versions - Latest release: 10 days ago - 3 dependent packages - 60.2 thousand downloads total - 1 maintainer
bnem 1.18.0
Training of logical models from indirect measurements of perturbation experiments6 versions - Latest release: about 2 months ago - 8.62 thousand downloads total - 2 stars on GitHub - 1 maintainer
primirTSS 1.28.0
Prediction of pri-miRNA Transcription Start Site6 versions - Latest release: about 1 month ago - 11.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
KBoost 1.18.0
Inference of gene regulatory networks from gene expression data6 versions - Latest release: about 1 month ago - 7.39 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 9.0% on bioconductor.org
6 versions - Latest release: about 1 month ago - 3 dependent packages - 39.3 thousand downloads total - 1 maintainer
RTN 2.34.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons6 versions - Latest release: about 1 month ago - 3 dependent packages - 39.3 thousand downloads total - 1 maintainer
MIRA 1.32.0
Methylation-Based Inference of Regulatory Activity6 versions - Latest release: about 1 month ago - 1 dependent package - 17.4 thousand downloads total - 1 maintainer
ribosomeProfilingQC 1.22.0
Ribosome Profiling Quality Control7 versions - Latest release: about 2 months ago - 12 thousand downloads total - 1 maintainer
AffiXcan 1.28.0
A Functional Approach To Impute Genetically Regulated Expression6 versions - Latest release: about 1 month ago - 15.4 thousand downloads total - 1 maintainer
Top 5.2% on bioconductor.org
7 versions - Latest release: about 1 month ago - 1 dependent package - 155 thousand downloads total - 1 maintainer
chromVAR 1.32.0
Chromatin Variation Across Regions7 versions - Latest release: about 1 month ago - 1 dependent package - 155 thousand downloads total - 1 maintainer
anota2seq 1.32.0
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq6 versions - Latest release: about 1 month ago - 22.1 thousand downloads total - 2 maintainers
MatrixRider 1.42.0
Obtain total affinity and occupancies for binding site matrices on a given sequence6 versions - Latest release: about 1 month ago - 18.9 thousand downloads total - 1 maintainer
diggit 1.42.0
Inference of Genetic Variants Driving Cellular Phenotypes6 versions - Latest release: about 1 month ago - 19.7 thousand downloads total - 1 maintainer
MethylMix 2.40.0
MethylMix: Identifying methylation driven cancer genes6 versions - Latest release: about 1 month ago - 29.7 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
6 versions - Latest release: about 1 month ago - 1 dependent package - 68 thousand downloads total - 3 stars on GitHub - 1 maintainer
qpgraph 2.44.0
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data6 versions - Latest release: about 1 month ago - 1 dependent package - 68 thousand downloads total - 3 stars on GitHub - 1 maintainer
GSReg 1.44.0
Gene Set Regulation (GS-Reg)6 versions - Latest release: about 1 month ago - 20.8 thousand downloads total - 2 maintainers
nullranges 1.16.3
Generation of null ranges via bootstrapping or covariate matching7 versions - Latest release: 10 days ago - 1 dependent package - 14.8 thousand downloads total - 22 stars on GitHub - 1 maintainer
GRENITS 1.62.0
Gene Regulatory Network Inference Using Time Series6 versions - Latest release: about 1 month ago - 29.4 thousand downloads total - 1 maintainer
tigre 1.64.0
Transcription factor Inference through Gaussian process Reconstruction of Expression6 versions - Latest release: about 2 months ago - 34.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
sRACIPE 2.2.0
Systems biology tool to simulate gene regulatory circuits7 versions - Latest release: about 1 month ago - 12.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
6 versions - Latest release: about 1 month ago - 49 thousand downloads total - 1 maintainer
BCRANK 1.72.0
Predicting binding site consensus from ranked DNA sequences6 versions - Latest release: about 1 month ago - 49 thousand downloads total - 1 maintainer
xcore 1.14.0
xcore expression regulators inference6 versions - Latest release: about 1 month ago - 6.93 thousand downloads total - 1 maintainer
universalmotif 1.28.0
Import, Modify, and Export Motifs with R9 versions - Latest release: about 1 month ago - 4 dependent packages - 74.7 thousand downloads total - 1 maintainer
INSPEcT 1.40.0
Modeling RNA synthesis, processing and degradation with RNA-seq data7 versions - Latest release: about 1 month ago - 24.4 thousand downloads total - 2 maintainers
GRaNIE 1.14.0
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...6 versions - Latest release: about 1 month ago - 9.43 thousand downloads total - 1 maintainer
blima 1.43.0
Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level6 versions - Latest release: about 1 month ago - 22.6 thousand downloads total - 1 maintainer
rifi 1.14.0
'rifi' analyses data from rifampicin time series created by microarray or RNAseq6 versions - Latest release: about 1 month ago - 6.46 thousand downloads total - 0 stars on GitHub - 1 maintainer
PIPETS 1.6.0
Poisson Identification of PEaks from Term-Seq data6 versions - Latest release: about 2 months ago - 4.56 thousand downloads total - 0 stars on GitHub - 1 maintainer
ISoLDE 1.38.0
Integrative Statistics of alleLe Dependent Expression6 versions - Latest release: about 1 month ago - 14.1 thousand downloads total - 1 maintainer
RTNduals 1.34.0
Analysis of co-regulation and inference of 'dual regulons'6 versions - Latest release: about 1 month ago - 1 dependent package - 16.5 thousand downloads total - 2 maintainers
pqsfinder 2.26.0
Identification of potential quadruplex forming sequences6 versions - Latest release: about 1 month ago - 23.2 thousand downloads total - 1 maintainer
ATACseqQC 1.34.0
ATAC-seq Quality Control6 versions - Latest release: about 1 month ago - 2 dependent packages - 64.3 thousand downloads total - 1 maintainer
proActiv 1.20.0
Estimate Promoter Activity from RNA-Seq data6 versions - Latest release: about 2 months ago - 11.3 thousand downloads total - 53 stars on GitHub - 1 maintainer
netZooR 1.14.0
A menagerie of methods for the inference and analysis of gene regulatory networks6 versions - Latest release: about 2 months ago - 6 thousand downloads total - 113 stars on GitHub - 1 maintainer
MIRit 1.6.1
Integrate microRNA and gene expression to decipher pathway complexity8 versions - Latest release: 10 days ago - 5.34 thousand downloads total - 1 stars on GitHub - 1 maintainer
dreamlet 1.8.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...7 versions - Latest release: about 2 months ago - 7.93 thousand downloads total - 20 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
6 versions - Latest release: about 2 months ago - 17 dependent packages - 463 thousand downloads total - 30 stars on GitHub - 1 maintainer
TFBSTools 1.48.0
Software Package for Transcription Factor Binding Site (TFBS) Analysis6 versions - Latest release: about 2 months ago - 17 dependent packages - 463 thousand downloads total - 30 stars on GitHub - 1 maintainer
rTRM 1.48.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks6 versions - Latest release: about 2 months ago - 1 dependent package - 27.9 thousand downloads total - 3 stars on GitHub - 1 maintainer
enhancerHomologSearch 1.16.0
Identification of putative mammalian orthologs to given enhancer8 versions - Latest release: about 1 month ago - 7.73 thousand downloads total - 0 stars on GitHub - 1 maintainer
projectR 1.26.0
Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering6 versions - Latest release: about 1 month ago - 1 dependent package - 13.8 thousand downloads total - 62 stars on GitHub - 1 maintainer
CRISPRseek 1.50.0
Design of guide RNAs in CRISPR genome-editing systems6 versions - Latest release: about 2 months ago - 3 dependent packages - 39.9 thousand downloads total - 1 maintainer
BioNERO 1.18.0
Biological Network Reconstruction Omnibus9 versions - Latest release: about 2 months ago - 1 dependent package - 23 thousand downloads total - 32 stars on GitHub - 1 maintainer
miRSM 2.6.0
Inferring miRNA sponge modules in heterogeneous data7 versions - Latest release: about 2 months ago - 11.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
terapadog 1.2.0
Translational Efficiency Regulation Analysis using the PADOG Method2 versions - Latest release: about 1 month ago - 2.41 thousand downloads total - 0 stars on GitHub - 1 maintainer
methylGSA 1.28.0
Gene Set Analysis Using the Outcome of Differential Methylation6 versions - Latest release: about 2 months ago - 19 thousand downloads total - 13 stars on GitHub - 1 maintainer
RIVER 1.34.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)6 versions - Latest release: about 2 months ago - 15.1 thousand downloads total - 10 stars on GitHub - 1 maintainer
DegCre 1.6.0
Probabilistic association of DEGs to CREs from differential data4 versions - Latest release: about 2 months ago - 5.01 thousand downloads total - 5 stars on GitHub - 1 maintainer
airpart 1.18.0
Differential cell-type-specific allelic imbalance6 versions - Latest release: about 2 months ago - 10.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
RNAdecay 1.30.0
Maximum Likelihood Decay Modeling of RNA Degradation Data8 versions - Latest release: about 2 months ago - 10.8 thousand downloads total - 1 maintainer
mpra 1.32.0
Analyze massively parallel reporter assays8 versions - Latest release: about 2 months ago - 15.8 thousand downloads total - 6 stars on GitHub - 1 maintainer
TFEA.ChIP 1.30.0
TFEA.ChIP, a Tool Kit for Transcription Factor Enrichment6 versions - Latest release: about 2 months ago - 16.2 thousand downloads total - 1 maintainer
LOLA 1.39.1
Locus overlap analysis for enrichment of genomic ranges6 versions - Latest release: about 2 months ago - 5 dependent packages - 40.1 thousand downloads total - 1 maintainer
epiregulon 2.0.2
Gene regulatory network inference from single cell epigenomic data6 versions - Latest release: 17 days ago - 1 dependent package - 4.68 thousand downloads total - 12 stars on GitHub - 1 maintainer
eisaR 1.22.1
Exon-Intron Split Analysis (EISA) in R7 versions - Latest release: about 2 months ago - 15.6 thousand downloads total - 16 stars on GitHub - 1 maintainer
Related Keywords
Software
123
GeneExpression
69
Transcription
44
Sequencing
42
DifferentialExpression
33
RNASeq
31
Network
28
ImmunoOncology
26
FunctionalGenomics
25
Transcriptomics
24
SystemsBiology
24
Regression
24
GeneSetEnrichment
22
Epigenetics
21
NetworkInference
21
Genetics
17
GraphAndNetwork
17
Coverage
14
DNAMethylation
14
Microarray
14
GeneTarget
14
Pathways
13
ATACSeq
12
SingleCell
12
ChIPSeq
12
Visualization
12
DataImport
11
NetworkEnrichment
11
DifferentialMethylation
11
Clustering
10
Bayesian
10
Normalization
10
Preprocessing
10
FunctionalPrediction
9
Annotation
8
QualityControl
8
MotifDiscovery
8
SNP
8
FeatureExtraction
7
KEGG
7
MethylationArray
7
GenomeAnnotation
7
GeneticVariability
7
MotifAnnotation
7
MultipleComparison
7
r
7
PeakDetection
7
Survival
6
AlternativeSplicing
6
SequenceMatching
6
StatisticalMethod
6
BiomedicalInformatics
6
DNaseSeq
5
TimeCourse
5
MethylSeq
5
CellBiology
5
Alignment
4
DNASeq
4
HistoneModification
4
DifferentialSplicing
4
genomics
4
bioconductor
4
GenomicVariation
4
Reactome
3
MathematicalBiology
3
Classification
3
DataRepresentation
3
PrincipalComponent
3
GO
3
RiboSeq
3
ThirdPartyClient
3
GenomeWideAssociation
3
CopyNumberVariation
3
ChipOnChip
3
BatchEffect
3
WorkflowStep
3
VariantAnnotation
3
rstats
2
DifferentialPeakCalling
2
RIPSeq
2
genetics
2
bioinformatics
2
HiddenMarkovModel
2
mirna
2
DimensionReduction
2
CRISPR
2
clustering
2
HiC
2
DNA3DStructure
2
TranscriptomeVariant
2
Proteomics
2
r-package
2
snp
1
generegulation
1
systemsbiology
1
genomicvariation
1
geneticvariability
1
mirnaseq-analysis
1
BiologicalQuestion
1
cerna
1