bioconductor.org "Epigenetics" keyword
monaLisa 1.18.0
Binned Motif Enrichment Analysis and Visualization10 versions - Latest release: 5 months ago - 24.8 thousand downloads total - 48 stars on GitHub - 1 maintainer
MIRit 1.8.0
Integrate microRNA and gene expression to decipher pathway complexity10 versions - Latest release: 4 months ago - 11.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
sevenC 1.32.0
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs7 versions - Latest release: 5 months ago - 22 thousand downloads total - 13 stars on GitHub - 1 maintainer
ENmix 1.48.3
Quality control and analysis tools for Illumina DNA methylation BeadChip14 versions - Latest release: 2 months ago - 57.7 thousand downloads total - 1 maintainer
CTexploreR 1.8.0
Explores Cancer Testis Genes5 versions - Latest release: 5 months ago - 10.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
SOMNiBUS 1.20.0
Smooth modeling of bisulfite sequencing8 versions - Latest release: 4 months ago - 12.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
dmrseq 1.32.0
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing10 versions - Latest release: 5 months ago - 1 dependent package - 42.1 thousand downloads total - 1 maintainer
epiRomics 1.0.0
Epigenomic Analysis Package Built for R (epiRomics)1 version - Latest release: 5 months ago - 3.01 thousand downloads total - 6 stars on GitHub - 1 maintainer
RBedMethyl 1.0.0
Disk-backed Representation of ONT bedMethyl Files1 version - Latest release: 5 months ago - 3.36 thousand downloads total - 0 stars on GitHub - 1 maintainer
BEAT 1.50.0
BEAT - BS-Seq Epimutation Analysis Toolkit7 versions - Latest release: 5 months ago - 33.3 thousand downloads total - 1 maintainer
mist 1.4.0
Differential Methylation Analysis for scDNAm Data4 versions - Latest release: 4 months ago - 6.53 thousand downloads total - 2 stars on GitHub - 1 maintainer
fCCAC 1.38.0
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing ...7 versions - Latest release: 4 months ago - 23.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
methylInheritance 1.36.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...8 versions - Latest release: 4 months ago - 1 dependent package - 23.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
epigraHMM 1.20.2
Epigenomic R-based analysis with hidden Markov models9 versions - Latest release: 4 months ago - 20.1 thousand downloads total - 1 maintainer
EpipwR 1.6.0
Efficient Power Analysis for EWAS with Continuous or Binary Outcomes4 versions - Latest release: 5 months ago - 6.18 thousand downloads total - 2 stars on GitHub - 1 maintainer
spatzie 1.18.0
Identification of enriched motif pairs from chromatin interaction data7 versions - Latest release: 5 months ago - 9.17 thousand downloads total - 1 maintainer
cliProfiler 1.18.0
A package for the CLIP data visualization7 versions - Latest release: 5 months ago - 13.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
m6Aboost 1.18.0
m6Aboost7 versions - Latest release: 4 months ago - 12.9 thousand downloads total - 3 stars on GitHub - 1 maintainer
tidyexposomics 1.0.0
Integrated Exposure-Omics Analysis Powered by Tidy Principles1 version - Latest release: 5 months ago - 4.47 thousand downloads total - 1 stars on GitHub - 1 maintainer
planet 1.20.0
Placental DNA methylation analysis tools7 versions - Latest release: 5 months ago - 1 dependent package - 21.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
AlphaBeta 1.26.0
Computational inference of epimutation rates and spectra from high-throughput DNA methylation dat...7 versions - Latest release: 5 months ago - 20.7 thousand downloads total - 1 maintainer
SPICEY 1.2.0
Calculates cell type specificity from single cell data2 versions - Latest release: 5 months ago - 4.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
mitch 1.24.0
Multi-Contrast Gene Set Enrichment Analysis10 versions - Latest release: 5 months ago - 18.9 thousand downloads total - 18 stars on GitHub - 1 maintainer
vmrseq 1.4.0
Probabilistic Modeling of Single-cell Methylation Heterogeneity4 versions - Latest release: 4 months ago - 6.32 thousand downloads total - 11 stars on GitHub - 1 maintainer
REMP 1.36.0
Repetitive Element Methylation Prediction4 versions - Latest release: about 1 month ago - 25.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
HiSpaR 1.0.0
Hierarchical Inference of Spatial Positions from Hi-C Data1 version - Latest release: 5 months ago - 2.49 thousand downloads total - 0 stars on GitHub - 1 maintainer
PoDCall 1.20.0
Positive Droplet Calling for DNA Methylation Droplet Digital PCR8 versions - Latest release: 4 months ago - 11 thousand downloads total - 1 maintainer
zenith 1.14.0
Gene set analysis following differential expression using linear (mixed) modeling with dream8 versions - Latest release: 5 months ago - 2 dependent packages - 18.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
methylscaper 1.20.0
Visualization of Methylation Data8 versions - Latest release: 4 months ago - 14.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
InTAD 1.32.0
Search for correlation between epigenetic signals and gene expression in TADs7 versions - Latest release: 5 months ago - 18.9 thousand downloads total - 1 maintainer
gVenn 1.1.1
Proportional Venn and UpSet Diagrams for Gene Sets and Genomic Regions2 versions - Latest release: 5 months ago - 7.27 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
9 versions - Latest release: 5 months ago - 31 dependent packages - 1.01 million downloads total - 64 stars on GitHub - 1 maintainer
minfi 1.58.0
Analyze Illumina Infinium DNA methylation arrays9 versions - Latest release: 5 months ago - 31 dependent packages - 1.01 million downloads total - 64 stars on GitHub - 1 maintainer
Motif2Site 1.16.0
Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across condi...7 versions - Latest release: 5 months ago - 18.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
30 versions - Latest release: 22 days ago - 181 dependent packages - 4.79 million downloads total - 4 maintainers
edgeR 4.10.5
Empirical Analysis of Digital Gene Expression Data in R30 versions - Latest release: 22 days ago - 181 dependent packages - 4.79 million downloads total - 4 maintainers
ISoLDE 1.40.0
Integrative Statistics of alleLe Dependent Expression7 versions - Latest release: 5 months ago - 22.6 thousand downloads total - 1 maintainer
chipenrich 2.36.0
Gene Set Enrichment For ChIP-seq Peak Data7 versions - Latest release: 4 months ago - 52.3 thousand downloads total - 1 maintainer
decemedip 1.0.0
hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methy...1 version - Latest release: 5 months ago - 6.91 thousand downloads total - 4 stars on GitHub - 1 maintainer
easier 1.18.0
Estimate Systems Immune Response from RNA-seq data7 versions - Latest release: 5 months ago - 22.9 thousand downloads total - 1 maintainer
damidBind 1.0.0
Differential Binding and Expression Analysis for DamID-seq Data1 version - Latest release: 5 months ago - 8.29 thousand downloads total - 1 maintainer
dinoR 1.8.0
Differential NOMe-seq analysis5 versions - Latest release: 5 months ago - 13 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
22 versions - Latest release: about 2 months ago - 322 dependent packages - 8.07 million downloads total - 1 maintainer
limma 3.68.5
Linear Models for Microarray and Omics Data22 versions - Latest release: about 2 months ago - 322 dependent packages - 8.07 million downloads total - 1 maintainer
crumblr 1.4.5
Count ratio uncertainty modeling base linear regression4 versions - Latest release: about 2 months ago - 10.8 thousand downloads total - 7 stars on GitHub - 1 maintainer
ramr 1.20.2
Detection of Rare Aberrantly Methylated Regions in Array and NGS Data8 versions - Latest release: 7 days ago - 20.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
variancePartition 1.42.0
Quantify and interpret drivers of variation in multilevel gene expression experiments13 versions - Latest release: 5 months ago - 4 dependent packages - 175 thousand downloads total - 16 stars on GitHub - 1 maintainer
knowYourCG 1.8.2
Functional analysis of DNA methylome datasets9 versions - Latest release: 7 days ago - 11.4 thousand downloads total - 6 stars on GitHub - 1 maintainer
dreamlet 1.10.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...8 versions - Latest release: 5 months ago - 22.2 thousand downloads total - 24 stars on GitHub - 1 maintainer
Chicago 1.40.0
CHiCAGO: Capture Hi-C Analysis of Genomic Organization7 versions - Latest release: 4 months ago - 39.1 thousand downloads total - 1 maintainer
Site2Target 1.4.0
An R package to associate peaks and target genes3 versions - Latest release: 5 months ago - 9.33 thousand downloads total - 1 maintainer
MethReg 1.21.0
Assessing the regulatory potential of DNA methylation regions or sites on gene transcription8 versions - Latest release: 5 months ago - 20.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
SingleMoleculeFootprinting 2.5.0
Analysis tools for Single Molecule Footprinting (SMF) data7 versions - Latest release: 4 months ago - 13.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
DEScan2 1.32.0
Differential Enrichment Scan 27 versions - Latest release: 5 months ago - 29.5 thousand downloads total - 1 maintainer
COCOA 2.26.0
Coordinate Covariation Analysis7 versions - Latest release: 4 months ago - 27.1 thousand downloads total - 1 maintainer
epialleleR 1.20.0
Fast, Accurate, Epiallele-Aware Methylation Caller and Reporter7 versions - Latest release: 5 months ago - 19.9 thousand downloads total - 7 stars on GitHub - 1 maintainer
RLSeq 1.6.0 removed
RLSeq: An analysis package for R-loop mapping data3 versions - Latest release: almost 3 years ago - 2.67 thousand downloads total - 2 stars on GitHub - 1 maintainer
MAGAR 1.20.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...7 versions - Latest release: 5 months ago - 19.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
epihet 1.16.0 removed
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data1 version - Latest release: almost 3 years ago - 4.09 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
8 versions - Latest release: about 2 months ago - 2 dependent packages - 334 thousand downloads total - 1 maintainer
DiffBind 3.22.2
Differential Binding Analysis of ChIP-Seq Peak Data8 versions - Latest release: about 2 months ago - 2 dependent packages - 334 thousand downloads total - 1 maintainer
idr2d 1.26.0
Irreproducible Discovery Rate for Genomic Interactions Data8 versions - Latest release: 5 months ago - 18.3 thousand downloads total - 1 maintainer
srnadiff 1.32.0
Finding differentially expressed unannotated genomic regions from RNA-seq data8 versions - Latest release: 5 months ago - 25.7 thousand downloads total - 1 maintainer
OMICsPCA 1.30.0
An R package for quantitative integration and analysis of multiple omics assays from heterogeneou...7 versions - Latest release: 5 months ago - 28.3 thousand downloads total - 1 maintainer
HiCaptuRe 1.2.0
HiCaptuRe: Manipulating and integrating Capture Hi-C data2 versions - Latest release: 5 months ago - 8.09 thousand downloads total - 3 stars on GitHub - 1 maintainer
metaseqR2 1.24.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...9 versions - Latest release: 4 months ago - 25.8 thousand downloads total - 1 maintainer
Top 10.0% on bioconductor.org
7 versions - Latest release: 4 months ago - 2 dependent packages - 77.2 thousand downloads total - 57 stars on GitHub - 1 maintainer
EpiDISH 2.28.0
Epigenetic Dissection of Intra-Sample-Heterogeneity7 versions - Latest release: 4 months ago - 2 dependent packages - 77.2 thousand downloads total - 57 stars on GitHub - 1 maintainer
compartmap 1.20.0 removed
Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seq3 versions - Latest release: almost 3 years ago - 6.72 thousand downloads total - 0 stars on GitHub - 1 maintainer
chromswitch 1.22.0 removed
An R package to detect chromatin state switches from epigenomic data1 version - Latest release: almost 3 years ago - 7.34 thousand downloads total - 5 stars on GitHub - 1 maintainer
TCseq 1.36.0
Time course sequencing data analysis7 versions - Latest release: 5 months ago - 54.4 thousand downloads total - 1 maintainer
MIRA 1.34.0
Methylation-Based Inference of Regulatory Activity7 versions - Latest release: 5 months ago - 1 dependent package - 29.8 thousand downloads total - 1 maintainer
msgbsR 1.36.0
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions7 versions - Latest release: 5 months ago - 19 thousand downloads total - 1 maintainer
methylSig 1.24.0
MethylSig: Differential Methylation Testing for WGBS and RRBS Data7 versions - Latest release: 4 months ago - 23 thousand downloads total - 15 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
15 versions - Latest release: 4 months ago - 2 dependent packages - 219 thousand downloads total - 1 maintainer
DMRcate 3.8.0
Methylation array and sequencing spatial analysis methods15 versions - Latest release: 4 months ago - 2 dependent packages - 219 thousand downloads total - 1 maintainer
scMET 1.14.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity7 versions - Latest release: 5 months ago - 16.6 thousand downloads total - 18 stars on GitHub - 1 maintainer
pathwayPCA 1.28.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection7 versions - Latest release: 4 months ago - 1 dependent package - 24.7 thousand downloads total - 11 stars on GitHub - 1 maintainer
mCSEA 1.32.0
Methylated CpGs Set Enrichment Analysis9 versions - Latest release: 5 months ago - 1 dependent package - 29.3 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
7 versions - Latest release: 5 months ago - 1 dependent package - 94.2 thousand downloads total - 1 maintainer
RnBeads 2.30.0
RnBeads7 versions - Latest release: 5 months ago - 1 dependent package - 94.2 thousand downloads total - 1 maintainer
omicRexposome 1.34.0
Exposome and omic data associatin and integration analysis8 versions - Latest release: 4 months ago - 26.9 thousand downloads total - 1 maintainer
netboost 2.20.0
Network Analysis Supported by Boosting8 versions - Latest release: 5 months ago - 16.5 thousand downloads total - 1 maintainer
betterChromVAR 1.0.3
Improved ChromVAR (Chromatin Variation Across Regions)2 versions - Latest release: 4 months ago - 4.16 thousand downloads total - 2 stars on GitHub - 1 maintainer
EpiMix 1.14.0
EpiMix: an integrative tool for the population-level analysis of DNA methylation7 versions - Latest release: 5 months ago - 1 dependent package - 15.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
TOAST 1.26.0
Tools for the analysis of heterogeneous tissues7 versions - Latest release: 5 months ago - 3 dependent packages - 50.5 thousand downloads total - 8 stars on GitHub - 1 maintainer
GAprediction 1.38.0
Prediction of gestational age with Illumina HumanMethylation450 data7 versions - Latest release: 5 months ago - 21.1 thousand downloads total - 1 maintainer
TRESS 1.18.0
Toolbox for mRNA epigenetics sequencing analysis7 versions - Latest release: 5 months ago - 1 dependent package - 17.2 thousand downloads total - 1 maintainer
cicero 1.30.0
Predict cis-co-accessibility from single-cell chromatin accessibility data8 versions - Latest release: 5 months ago - 50.4 thousand downloads total - 1 maintainer
xcore 1.16.0
xcore expression regulators inference7 versions - Latest release: 4 months ago - 15.2 thousand downloads total - 1 maintainer
CTdata 1.12.0
Data companion to CTexploreR7 versions - Latest release: 5 months ago - 1 dependent package - 13.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
methimpute 1.34.0
Imputation-guided re-construction of complete methylomes from WGBS data7 versions - Latest release: 4 months ago - 24.8 thousand downloads total - 1 maintainer
MethPed 1.40.0
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes7 versions - Latest release: 5 months ago - 26.7 thousand downloads total - 1 maintainer
nuCpos 1.30.0
An R package for prediction of nucleosome positions7 versions - Latest release: 5 months ago - 17.8 thousand downloads total - 1 maintainer
omicsPrint 1.32.0
Cross omic genetic fingerprinting7 versions - Latest release: 4 months ago - 23.7 thousand downloads total - 1 maintainer
roastgsa 1.10.0
Rotation based gene set analysis6 versions - Latest release: 4 months ago - 11.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
proActiv 1.22.0
Estimate Promoter Activity from RNA-Seq data7 versions - Latest release: 5 months ago - 19 thousand downloads total - 59 stars on GitHub - 1 maintainer
MEAT 1.24.0
Muscle Epigenetic Age Test7 versions - Latest release: 4 months ago - 18.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
epidecodeR 1.20.0
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation7 versions - Latest release: 5 months ago - 14.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
7 versions - Latest release: 4 months ago - 15 dependent packages - 614 thousand downloads total - 18 stars on GitHub - 1 maintainer
bumphunter 1.54.0
Bump Hunter7 versions - Latest release: 4 months ago - 15 dependent packages - 614 thousand downloads total - 18 stars on GitHub - 1 maintainer
atacInferCnv 1.0.0
Call CNV from single cell ATAC-seq data based on InferCNV adaptation2 versions - Latest release: 2 months ago - 3.19 thousand downloads total - 0 stars on GitHub - 1 maintainer
EpiCompare 1.16.0
Comparison, Benchmarking & QC of Epigenomic Datasets16 versions - Latest release: 5 months ago - 13.2 thousand downloads total - 19 stars on GitHub - 1 maintainer
methInheritSim 1.34.0
Simulating Whole-Genome Inherited Bisulphite Sequencing Data7 versions - Latest release: 4 months ago - 1 dependent package - 22.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
coMethDMR 1.16.0
Accurate identification of co-methylated and differentially methylated regions in epigenome-wide ...7 versions - Latest release: 5 months ago - 14.5 thousand downloads total - 7 stars on GitHub - 1 maintainer
recountmethylation 1.22.0
Access and analyze public DNA methylation array data compilations7 versions - Latest release: 4 months ago - 17.9 thousand downloads total - 9 stars on GitHub - 1 maintainer
nullranges 1.18.0
Generation of null ranges via bootstrapping or covariate matching8 versions - Latest release: 5 months ago - 1 dependent package - 22.9 thousand downloads total - 29 stars on GitHub - 1 maintainer
TENET 1.4.0
R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key...4 versions - Latest release: 5 months ago - 6.98 thousand downloads total - 1 stars on GitHub - 1 maintainer
Related Keywords
Software
114
DNAMethylation
51
Sequencing
48
ImmunoOncology
44
GeneExpression
35
DifferentialMethylation
33
FunctionalGenomics
29
Regression
26
Transcription
24
GeneRegulation
23
Transcriptomics
22
DifferentialExpression
22
RNASeq
21
Genetics
21
Preprocessing
20
QualityControl
20
ChIPSeq
20
MethylSeq
19
MultipleComparison
19
MethylationArray
19
DataImport
18
SingleCell
18
Microarray
16
Clustering
16
ATACSeq
14
GeneSetEnrichment
14
Coverage
14
Visualization
14
Normalization
14
BiomedicalInformatics
13
BatchEffect
12
SystemsBiology
10
GeneTarget
9
bioconductor
9
Classification
9
Bayesian
9
TwoChannel
9
HiC
8
CellBiology
7
HistoneModification
7
Proteomics
7
Pathways
6
FeatureExtraction
6
TimeCourse
6
WholeGenome
6
DimensionReduction
6
GenomeAnnotation
6
DNaseSeq
6
r-package
6
StatisticalMethod
6
Annotation
5
r
5
CpGIsland
5
AlternativeSplicing
5
DifferentialPeakCalling
5
PeakDetection
5
DifferentialSplicing
5
PrincipalComponent
5
epigenomics
5
Survival
4
bioinformatics
4
ExperimentHubSoftware
4
GenomeWideAssociation
4
epigenetics
4
chip-seq
4
SNP
4
GeneticVariability
4
NucleosomePositioning
4
Metabolomics
4
dna-methylation
4
DataRepresentation
4
OneChannel
4
HiddenMarkovModel
3
DNA3DStructure
3
MultiChannel
3
ReportWriting
3
BiologicalQuestion
3
GraphAndNetwork
3
genomics
3
WorkflowStep
3
ProprietaryPlatforms
3
mRNAMicroarray
3
CopyNumberVariation
3
Network
3
MicroRNAArray
2
GenomicVariation
2
ExonArray
2
MathematicalBiology
2
Infrastructure
2
genetics
2
bioconductor-package
2
transcription-factors
2
RIPSeq
2
Cheminformatics
2
FunctionalPrediction
2
single-cell
2
ResearchField
2
Spatial
2
SequenceMatching
2
LongRead
2