bioconductor.org "GeneRegulation" keyword
View the packages on the bioconductor.org package registry that are tagged with the "GeneRegulation" keyword.
rigvf 1.0.2
R interface to the IGVF Catalog2 versions - Latest release: about 1 month ago - 1.21 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
7 versions - Latest release: 3 months ago - 14 dependent packages - 363 thousand downloads total - 2 maintainers
Rsubread 2.22.1
Mapping, quantification and variant analysis of sequencing data7 versions - Latest release: 3 months ago - 14 dependent packages - 363 thousand downloads total - 2 maintainers
netZooR 1.11.0
Unified methods for the inference and analysis of gene regulatory networks5 versions - Latest release: 3 months ago - 5.48 thousand downloads total - 109 stars on GitHub - 1 maintainer
miRSM 2.4.0
Inferring miRNA sponge modules in heterogeneous data6 versions - Latest release: 3 months ago - 10.2 thousand downloads total - 4 stars on GitHub - 1 maintainer
nullranges 1.14.0
Generation of null ranges via bootstrapping or covariate matching5 versions - Latest release: 2 months ago - 1 dependent package - 11 thousand downloads total - 22 stars on GitHub - 1 maintainer
terapadog 1.0.0
Translational Efficiency Regulation Analysis using the PADOG Method1 version - Latest release: 3 months ago - 1.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
GRENITS 1.60.0
Gene Regulatory Network Inference Using Time Series5 versions - Latest release: 3 months ago - 27.6 thousand downloads total - 1 maintainer
epidecodeR 1.16.0
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation5 versions - Latest release: 3 months ago - 6.74 thousand downloads total - 3 stars on GitHub - 1 maintainer
seqArchR 1.12.0
Identify Different Architectures of Sequence Elements5 versions - Latest release: 3 months ago - 1 dependent package - 6.34 thousand downloads total - 1 stars on GitHub - 1 maintainer
xcore 1.12.0
xcore expression regulators inference5 versions - Latest release: 2 months ago - 5.56 thousand downloads total - 1 maintainer
RIVER 1.32.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)5 versions - Latest release: 3 months ago - 13.5 thousand downloads total - 10 stars on GitHub - 1 maintainer
APAlyzer 1.22.0
A toolkit for APA analysis using RNA-seq data5 versions - Latest release: 2 months ago - 11.6 thousand downloads total - 4 stars on GitHub - 1 maintainer
BioNERO 1.16.0
Biological Network Reconstruction Omnibus7 versions - Latest release: 3 months ago - 1 dependent package - 19.8 thousand downloads total - 29 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
7 versions - Latest release: 2 months ago - 7 dependent packages - 474 thousand downloads total - 321 stars on GitHub - 2 maintainers
TCGAbiolinks 2.36.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data7 versions - Latest release: 2 months ago - 7 dependent packages - 474 thousand downloads total - 321 stars on GitHub - 2 maintainers
ATACseqQC 1.32.0
ATAC-seq Quality Control5 versions - Latest release: 2 months ago - 2 dependent packages - 56.8 thousand downloads total - 1 maintainer
memes 1.16.0
motif matching, comparison, and de novo discovery using the MEME Suite5 versions - Latest release: 3 months ago - 17.2 thousand downloads total - 43 stars on GitHub - 1 maintainer
proActiv 1.18.0
Estimate Promoter Activity from RNA-Seq data5 versions - Latest release: 2 months ago - 8.72 thousand downloads total - 53 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
5 versions - Latest release: 2 months ago - 17 dependent packages - 392 thousand downloads total - 29 stars on GitHub - 1 maintainer
TFBSTools 1.46.0
Software Package for Transcription Factor Binding Site (TFBS) Analysis5 versions - Latest release: 2 months ago - 17 dependent packages - 392 thousand downloads total - 29 stars on GitHub - 1 maintainer
GSReg 1.42.0
Gene Set Regulation (GS-Reg)5 versions - Latest release: 2 months ago - 19 thousand downloads total - 2 maintainers
diggit 1.40.0
Inference of Genetic Variants Driving Cellular Phenotypes5 versions - Latest release: 2 months ago - 17.9 thousand downloads total - 1 maintainer
regutools 1.20.0
regutools: an R package for data extraction from RegulonDB5 versions - Latest release: 2 months ago - 8.67 thousand downloads total - 5 stars on GitHub - 1 maintainer
GSRI 2.56.0
Gene Set Regulation Index5 versions - Latest release: 3 months ago - 30.7 thousand downloads total - 1 maintainer
INSPEcT 1.38.0
Modeling RNA synthesis, processing and degradation with RNA-seq data6 versions - Latest release: 3 months ago - 21.3 thousand downloads total - 2 maintainers
PIPETS 1.4.0
Poisson Identification of PEaks from Term-Seq data5 versions - Latest release: 3 months ago - 3.37 thousand downloads total - 0 stars on GitHub - 1 maintainer
sarks 1.20.0
Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains5 versions - Latest release: 3 months ago - 7.71 thousand downloads total - 1 maintainer
TENET 1.0.1
R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key...2 versions - Latest release: about 2 months ago - 937 downloads total - 1 stars on GitHub - 1 maintainer
cicero 1.26.0
Predict cis-co-accessibility from single-cell chromatin accessibility data5 versions - Latest release: 3 months ago - 30.2 thousand downloads total - 1 maintainer
geneplast 1.34.0
Evolutionary and plasticity analysis of orthologous groups5 versions - Latest release: 3 months ago - 1 dependent package - 16.1 thousand downloads total - 1 maintainer
AffiXcan 1.26.0
A Functional Approach To Impute Genetically Regulated Expression5 versions - Latest release: 3 months ago - 13.7 thousand downloads total - 1 maintainer
OmnipathR 3.16.0
OmniPath web service client and more7 versions - Latest release: 3 months ago - 3 dependent packages - 44 thousand downloads total - 1 maintainer
universalmotif 1.26.2
Import, Modify, and Export Motifs with R7 versions - Latest release: 3 months ago - 4 dependent packages - 55.3 thousand downloads total - 1 maintainer
BindingSiteFinder 2.6.0
Binding site defintion based on iCLIP data5 versions - Latest release: 3 months ago - 6.69 thousand downloads total - 3 stars on GitHub - 1 maintainer
projectR 1.24.0
Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering5 versions - Latest release: 3 months ago - 1 dependent package - 11.4 thousand downloads total - 62 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 43 thousand downloads total - 2 maintainers
GDCRNATools 1.28.0
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data i...5 versions - Latest release: 3 months ago - 43 thousand downloads total - 2 maintainers
IMAS 1.32.0
Integrative analysis of Multi-omics data for Alternative Splicing5 versions - Latest release: 3 months ago - 13.9 thousand downloads total - 1 maintainer
decoupleR 2.14.0
decoupleR: Ensemble of computational methods to infer biological activities from omics data6 versions - Latest release: 2 months ago - 3 dependent packages - 54.6 thousand downloads total - 256 stars on GitHub - 1 maintainer
idr2d 1.22.0
Irreproducible Discovery Rate for Genomic Interactions Data5 versions - Latest release: 3 months ago - 9.21 thousand downloads total - 1 maintainer
ATACseqTFEA 1.10.0
Transcription Factor Enrichment Analysis for ATAC-seq5 versions - Latest release: 3 months ago - 5.51 thousand downloads total - 1 stars on GitHub - 1 maintainer
MIRit 1.4.1
Integrate microRNA and gene expression to decipher pathway complexity5 versions - Latest release: about 2 months ago - 3.69 thousand downloads total - 1 stars on GitHub - 1 maintainer
rifiComparative 1.8.0
'rifiComparative' compares the output of rifi from two different conditions.5 versions - Latest release: 3 months ago - 4.15 thousand downloads total - 0 stars on GitHub - 1 maintainer
eisaR 1.20.0
Exon-Intron Split Analysis (EISA) in R6 versions - Latest release: 3 months ago - 12.8 thousand downloads total - 16 stars on GitHub - 1 maintainer
bnem 1.16.0
Training of logical models from indirect measurements of perturbation experiments5 versions - Latest release: 3 months ago - 7.04 thousand downloads total - 2 stars on GitHub - 1 maintainer
LOLA 1.38.0
Locus overlap analysis for enrichment of genomic ranges5 versions - Latest release: 3 months ago - 5 dependent packages - 31.3 thousand downloads total - 1 maintainer
rTRM 1.46.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks5 versions - Latest release: 3 months ago - 1 dependent package - 25.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
mpra 1.30.1
Analyze massively parallel reporter assays7 versions - Latest release: about 2 months ago - 13.1 thousand downloads total - 6 stars on GitHub - 1 maintainer
RNAdecay 1.28.0
Maximum Likelihood Decay Modeling of RNA Degradation Data7 versions - Latest release: 3 months ago - 9.36 thousand downloads total - 1 maintainer
epiregulon 1.4.0
Gene regulatory network inference from single cell epigenomic data4 versions - Latest release: 3 months ago - 1 dependent package - 3.07 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 7 dependent packages - 72.6 thousand downloads total - 1 maintainer
viper 1.42.0
Virtual Inference of Protein-activity by Enriched Regulon analysis5 versions - Latest release: 3 months ago - 7 dependent packages - 72.6 thousand downloads total - 1 maintainer
tRanslatome 1.46.0
Comparison between multiple levels of gene expression5 versions - Latest release: 3 months ago - 25.3 thousand downloads total - 2 maintainers
Top 4.6% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 61.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
qpgraph 2.42.0
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data5 versions - Latest release: 3 months ago - 1 dependent package - 61.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
profileScoreDist 1.36.0
Profile score distributions5 versions - Latest release: 3 months ago - 12.8 thousand downloads total - 1 maintainer
BasicSTARRseq 1.36.0
Basic peak calling on STARR-seq data5 versions - Latest release: 3 months ago - 17.3 thousand downloads total - 1 maintainer
Cogito 1.14.0
Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic...5 versions - Latest release: 3 months ago - 5.9 thousand downloads total - 1 maintainer
CRISPRseek 1.48.0
Design of guide RNAs in CRISPR genome-editing systems5 versions - Latest release: 3 months ago - 3 dependent packages - 34.1 thousand downloads total - 1 maintainer
rTRMui 1.46.0
A shiny user interface for rTRM5 versions - Latest release: 3 months ago - 21.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
Melissa 1.24.0
Bayesian clustering and imputationa of single cell methylomes5 versions - Latest release: 3 months ago - 9.22 thousand downloads total - 1 maintainer
scMET 1.10.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity5 versions - Latest release: 3 months ago - 4.97 thousand downloads total - 18 stars on GitHub - 1 maintainer
IVAS 2.28.0
Identification of genetic Variants affecting Alternative Splicing5 versions - Latest release: 3 months ago - 1 dependent package - 18.6 thousand downloads total - 1 maintainer
KBoost 1.16.0
Inference of gene regulatory networks from gene expression data5 versions - Latest release: 3 months ago - 5.93 thousand downloads total - 4 stars on GitHub - 1 maintainer
epiregulon.extra 1.4.0
Companion package to epiregulon with additional plotting, differential and graph functions6 versions - Latest release: 3 months ago - 3.41 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
6 versions - Latest release: about 2 months ago - 1 dependent package - 123 thousand downloads total - 1 maintainer
chromVAR 1.30.1
Chromatin Variation Across Regions6 versions - Latest release: about 2 months ago - 1 dependent package - 123 thousand downloads total - 1 maintainer
BiFET 1.28.0
Bias-free Footprint Enrichment Test5 versions - Latest release: 3 months ago - 14.5 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 3 dependent packages - 34.9 thousand downloads total - 1 maintainer
RTN 2.32.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons5 versions - Latest release: 3 months ago - 3 dependent packages - 34.9 thousand downloads total - 1 maintainer
sRACIPE 2.0.1
Systems biology tool to simulate gene regulatory circuits6 versions - Latest release: about 2 months ago - 9.52 thousand downloads total - 0 stars on GitHub - 1 maintainer
AMARETTO 1.24.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...5 versions - Latest release: 3 months ago - 14.2 thousand downloads total - 1 maintainer
Top 3.6% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 280 thousand downloads total - 3 stars on GitHub - 1 maintainer
CNEr 1.43.0
CNE Detection and Visualization5 versions - Latest release: 3 months ago - 1 dependent package - 280 thousand downloads total - 3 stars on GitHub - 1 maintainer
methylGSA 1.26.0
Gene Set Analysis Using the Outcome of Differential Methylation5 versions - Latest release: 3 months ago - 16.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
GUIDEseq 1.38.0
GUIDE-seq and PEtag-seq analysis pipeline5 versions - Latest release: 3 months ago - 1 dependent package - 18.8 thousand downloads total - 1 maintainer
spatzie 1.14.0
Identification of enriched motif pairs from chromatin interaction data5 versions - Latest release: 3 months ago - 5.65 thousand downloads total - 1 maintainer
tigre 1.62.0
Transcription factor Inference through Gaussian process Reconstruction of Expression5 versions - Latest release: 3 months ago - 31.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
triplex 1.48.0
Search and visualize intramolecular triplex-forming sequences in DNA5 versions - Latest release: 3 months ago - 24.3 thousand downloads total - 1 maintainer
GRaNIE 1.12.0
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...5 versions - Latest release: 3 months ago - 7.59 thousand downloads total - 1 maintainer
BUMHMM 1.32.0
Computational pipeline for computing probability of modification from structure probing experimen...5 versions - Latest release: 3 months ago - 13.9 thousand downloads total - 1 maintainer
MethylMix 2.38.0
MethylMix: Identifying methylation driven cancer genes5 versions - Latest release: 3 months ago - 27.2 thousand downloads total - 1 maintainer
NADfinder 1.32.0
Call wide peaks for sequencing data5 versions - Latest release: 3 months ago - 14.1 thousand downloads total - 2 maintainers
SELEX 1.40.0
Functions for analyzing SELEX-seq data5 versions - Latest release: 3 months ago - 17.2 thousand downloads total - 1 maintainer
MoonlightR 1.34.0
Identify oncogenes and tumor suppressor genes from omics data5 versions - Latest release: 3 months ago - 16.1 thousand downloads total - 17 stars on GitHub - 1 maintainer
pqsfinder 2.24.0
Identification of potential quadruplex forming sequences5 versions - Latest release: 3 months ago - 18.1 thousand downloads total - 1 maintainer
Top 2.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 2 dependent packages - 266 thousand downloads total - 1 maintainer
DiffBind 3.18.0
Differential Binding Analysis of ChIP-Seq Peak Data5 versions - Latest release: 3 months ago - 2 dependent packages - 266 thousand downloads total - 1 maintainer
pandaR 1.40.0
PANDA Algorithm5 versions - Latest release: 3 months ago - 1 dependent package - 21.8 thousand downloads total - 2 maintainers
rifi 1.12.0
'rifi' analyses data from rifampicin time series created by microarray or RNAseq5 versions - Latest release: 3 months ago - 5.04 thousand downloads total - 0 stars on GitHub - 1 maintainer
MatrixRider 1.40.0
Obtain total affinity and occupancies for binding site matrices on a given sequence5 versions - Latest release: 3 months ago - 16.6 thousand downloads total - 1 maintainer
GenomicOZone 1.22.0
Delineate outstanding genomic zones of differential gene activity5 versions - Latest release: 3 months ago - 9.18 thousand downloads total - 1 maintainer
Top 7.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 44.3 thousand downloads total - 1 maintainer
ELMER 2.32.0
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes5 versions - Latest release: 3 months ago - 44.3 thousand downloads total - 1 maintainer
RiboDiPA 1.16.0
Differential pattern analysis for Ribo-seq data5 versions - Latest release: 3 months ago - 7.06 thousand downloads total - 1 maintainer
SPONGE 1.30.0
Sparse Partial Correlations On Gene Expression6 versions - Latest release: 3 months ago - 2 dependent packages - 12.3 thousand downloads total - 1 maintainer
omicRexposome 1.30.0
Exposome and omic data associatin and integration analysis6 versions - Latest release: 3 months ago - 12.6 thousand downloads total - 1 maintainer
airpart 1.16.0
Differential cell-type-specific allelic imbalance5 versions - Latest release: 3 months ago - 8.99 thousand downloads total - 2 stars on GitHub - 1 maintainer
Moonlight2R 1.6.0
Identify oncogenes and tumor suppressor genes from omics data4 versions - Latest release: 3 months ago - 4.08 thousand downloads total - 5 stars on GitHub - 1 maintainer
CAGEfightR 1.28.0
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor5 versions - Latest release: 3 months ago - 1 dependent package - 25.5 thousand downloads total - 8 stars on GitHub - 1 maintainer
COCOA 2.22.0
Coordinate Covariation Analysis5 versions - Latest release: 3 months ago - 11.2 thousand downloads total - 1 maintainer
ISoLDE 1.36.0
Integrative Statistics of alleLe Dependent Expression5 versions - Latest release: 3 months ago - 12.5 thousand downloads total - 1 maintainer
anota2seq 1.30.0
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq5 versions - Latest release: 3 months ago - 18 thousand downloads total - 2 maintainers
MIRA 1.30.0
Methylation-Based Inference of Regulatory Activity5 versions - Latest release: 3 months ago - 1 dependent package - 14.5 thousand downloads total - 1 maintainer
RTNsurvival 1.32.0
Survival analysis using transcriptional networks inferred by the RTN package5 versions - Latest release: 3 months ago - 13 thousand downloads total - 2 maintainers
RTNduals 1.32.0
Analysis of co-regulation and inference of 'dual regulons'5 versions - Latest release: 3 months ago - 1 dependent package - 14.4 thousand downloads total - 2 maintainers
GIGSEA 1.26.0
Genotype Imputed Gene Set Enrichment Analysis5 versions - Latest release: 3 months ago - 9.19 thousand downloads total - 1 maintainer
TFEA.ChIP 1.28.0
Analyze Transcription Factor Enrichment5 versions - Latest release: 3 months ago - 13.7 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
5 versions - Latest release: 3 months ago - 43.8 thousand downloads total - 1 maintainer
BCRANK 1.70.0
Predicting binding site consensus from ranked DNA sequences5 versions - Latest release: 3 months ago - 43.8 thousand downloads total - 1 maintainer
BPRMeth 1.34.0
Model higher-order methylation profiles5 versions - Latest release: 3 months ago - 1 dependent package - 16.4 thousand downloads total - 1 maintainer
Related Keywords
Software
121
GeneExpression
67
Transcription
43
Sequencing
41
DifferentialExpression
32
RNASeq
30
Network
27
ImmunoOncology
26
FunctionalGenomics
25
Regression
24
SystemsBiology
24
Transcriptomics
23
GeneSetEnrichment
21
NetworkInference
20
Epigenetics
20
Genetics
17
GraphAndNetwork
16
Microarray
14
DNAMethylation
14
Coverage
14
GeneTarget
13
ATACSeq
12
Pathways
12
ChIPSeq
12
Visualization
11
DataImport
11
DifferentialMethylation
11
Clustering
10
SingleCell
10
Bayesian
10
Preprocessing
10
NetworkEnrichment
10
Normalization
10
FunctionalPrediction
9
MotifDiscovery
8
SNP
8
QualityControl
8
Annotation
8
GenomeAnnotation
7
r
7
PeakDetection
7
MultipleComparison
7
MotifAnnotation
7
GeneticVariability
7
MethylationArray
7
FeatureExtraction
7
BiomedicalInformatics
6
Survival
6
KEGG
6
AlternativeSplicing
6
StatisticalMethod
6
SequenceMatching
6
CellBiology
5
MethylSeq
5
DNaseSeq
5
TimeCourse
5
DNASeq
4
GenomicVariation
4
DifferentialSplicing
4
genomics
4
bioconductor
4
HistoneModification
4
Alignment
4
WorkflowStep
3
CopyNumberVariation
3
BatchEffect
3
ThirdPartyClient
3
VariantAnnotation
3
MathematicalBiology
3
GO
3
Classification
3
PrincipalComponent
3
DataRepresentation
3
GenomeWideAssociation
3
RiboSeq
3
mirna
2
RIPSeq
2
DNA3DStructure
2
HiC
2
CRISPR
2
genetics
2
HiddenMarkovModel
2
Proteomics
2
Reactome
2
DimensionReduction
2
TranscriptomeVariant
2
clustering
2
rstats
2
bioinformatics
2
r-package
2
ChipOnChip
2
mirnaseq-analysis
1
hierarchical-models
1
heterogeneity
1
generalised-linear-models
1
bayesian-inference
1
GUI
1
mirna-seq
1
Regulation
1
Bioinformatics
1