bioconductor.org "DifferentialMethylation" keyword
View the packages on the bioconductor.org package registry that are tagged with the "DifferentialMethylation" keyword.
DAMEfinder 1.20.0
Finds DAMEs - Differential Allelicly MEthylated regions5 versions - Latest release: 3 months ago - 11.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
6 versions - Latest release: 3 months ago - 5 dependent packages - 151 thousand downloads total - 4 maintainers
missMethyl 1.42.0
Analysing Illumina HumanMethylation BeadChip Data6 versions - Latest release: 3 months ago - 5 dependent packages - 151 thousand downloads total - 4 maintainers
Top 1.9% on bioconductor.org
7 versions - Latest release: 3 months ago - 31 dependent packages - 850 thousand downloads total - 60 stars on GitHub - 1 maintainer
minfi 1.54.1
Analyze Illumina Infinium DNA methylation arrays7 versions - Latest release: 3 months ago - 31 dependent packages - 850 thousand downloads total - 60 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
23 versions - Latest release: 16 days ago - 181 dependent packages - 3.6 million downloads total - 4 maintainers
edgeR 4.6.3
Empirical Analysis of Digital Gene Expression Data in R23 versions - Latest release: 16 days ago - 181 dependent packages - 3.6 million downloads total - 4 maintainers
DMCHMM 1.30.1
Differentially Methylated CpG using Hidden Markov Model5 versions - Latest release: 2 months ago - 12.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
planet 1.16.0
Placental DNA methylation analysis tools5 versions - Latest release: 3 months ago - 1 dependent package - 11.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
12 versions - Latest release: 3 months ago - 2 dependent packages - 166 thousand downloads total - 1 maintainer
DMRcate 3.4.0
Methylation array and sequencing spatial analysis methods12 versions - Latest release: 3 months ago - 2 dependent packages - 166 thousand downloads total - 1 maintainer
Top 10.0% on bioconductor.org
5 versions - Latest release: 2 months ago - 2 dependent packages - 43.7 thousand downloads total - 50 stars on GitHub - 1 maintainer
EpiDISH 2.24.0
Epigenetic Dissection of Intra-Sample-Heterogeneity5 versions - Latest release: 2 months ago - 2 dependent packages - 43.7 thousand downloads total - 50 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
betaHMM 1.4.1
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Be...4 versions - Latest release: 2 months ago - 3.39 thousand downloads total - 1 maintainer
NanoMethViz 3.4.0
Visualise methylation data from Oxford Nanopore sequencing5 versions - Latest release: 3 months ago - 10.6 thousand downloads total - 28 stars on GitHub - 1 maintainer
Top 8.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 30.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
regionReport 1.42.0
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results5 versions - Latest release: 3 months ago - 1 dependent package - 30.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
MAGAR 1.16.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...5 versions - Latest release: 2 months ago - 8.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
TOAST 1.22.0
Tools for the analysis of heterogeneous tissues5 versions - Latest release: 3 months ago - 3 dependent packages - 28.4 thousand downloads total - 8 stars on GitHub - 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
spiky 1.14.0
Spike-in calibration for cell-free MeDIP5 versions - Latest release: 2 months ago - 6.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
DMCFB 1.22.1
Differentially Methylated Cytosines via a Bayesian Functional Approach7 versions - Latest release: about 2 months ago - 8.75 thousand downloads total - 0 stars on GitHub - 1 maintainer
Damsel 1.4.0
Damsel: an end to end analysis of DamID4 versions - Latest release: 3 months ago - 2.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
ramr 1.16.0
Detection of Rare Aberrantly Methylated Regions in Array and NGS Data5 versions - Latest release: 3 months ago - 7.14 thousand downloads total - 0 stars on GitHub - 1 maintainer
EpiMix 1.10.0
EpiMix: an integrative tool for the population-level analysis of DNA methylation5 versions - Latest release: 3 months ago - 1 dependent package - 5.11 thousand downloads total - 1 stars on GitHub - 1 maintainer
cfTools 1.8.0
Informatics Tools for Cell-Free DNA Study5 versions - Latest release: 2 months ago - 4.38 thousand downloads total - 6 stars on GitHub - 1 maintainer
nempi 1.16.0
Inferring unobserved perturbations from gene expression data5 versions - Latest release: 3 months ago - 6.41 thousand downloads total - 2 stars on GitHub - 1 maintainer
magpie 1.8.0
MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation5 versions - Latest release: 3 months ago - 4.32 thousand downloads total - 0 stars on GitHub - 1 maintainer
dmrseq 1.28.0
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing8 versions - Latest release: 3 months ago - 1 dependent package - 26.8 thousand downloads total - 1 maintainer
coMethDMR 1.12.0
Accurate identification of co-methylated and differentially methylated regions in epigenome-wide ...5 versions - Latest release: 3 months ago - 6.08 thousand downloads total - 7 stars on GitHub - 1 maintainer
HIREewas 1.26.0
Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies5 versions - Latest release: 3 months ago - 9.55 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
regionalpcs 1.6.0
Summarizing Regional Methylation with Regional Principal Components Analysis4 versions - Latest release: 3 months ago - 4.21 thousand downloads total - 3 stars on GitHub - 1 maintainer
methInheritSim 1.30.0
Simulating Whole-Genome Inherited Bisulphite Sequencing Data5 versions - Latest release: 3 months ago - 1 dependent package - 12.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
shinyepico 1.16.0
ShinyÉPICo5 versions - Latest release: 3 months ago - 7.28 thousand downloads total - 5 stars on GitHub - 1 maintainer
IWTomics 1.32.0
Interval-Wise Testing for Omics Data5 versions - Latest release: 3 months ago - 14.1 thousand downloads total - 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
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
Top 4.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 65.6 thousand downloads total - 1 maintainer
RnBeads 2.26.0
RnBeads5 versions - Latest release: 3 months ago - 1 dependent package - 65.6 thousand downloads total - 1 maintainer
borealis 1.12.0
Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution5 versions - Latest release: 3 months ago - 5.25 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
SMITE 1.36.0
Significance-based Modules Integrating the Transcriptome and Epigenome5 versions - Latest release: 3 months ago - 15.8 thousand downloads total - 1 stars on GitHub - 2 maintainers
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
ramwas 1.32.0
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms5 versions - Latest release: 3 months ago - 16.8 thousand downloads total - 1 maintainer
GeoTcgaData 2.8.0
Processing Various Types of Data on GEO and TCGA5 versions - Latest release: 3 months ago - 6.23 thousand downloads total - 26 stars on GitHub - 1 maintainer
ENmix 1.44.1
Quality control and analysis tools for Illumina DNA methylation BeadChip8 versions - Latest release: about 2 months ago - 37.6 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
msgbsR 1.32.0
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions5 versions - Latest release: 3 months ago - 13 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
DMRcaller 1.40.0
Differentially Methylated Regions caller5 versions - Latest release: 3 months ago - 22.9 thousand downloads total - 1 maintainer
SIMD 1.26.0
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site5 versions - Latest release: 3 months ago - 9.35 thousand downloads total - 1 maintainer
PoDCall 1.16.0
Positive Droplet Calling for DNA Methylation Droplet Digital PCR6 versions - Latest release: 3 months ago - 5.63 thousand downloads total - 1 maintainer
methylSig 1.20.0
MethylSig: Differential Methylation Testing for WGBS and RRBS Data5 versions - Latest release: 3 months ago - 9.19 thousand downloads total - 15 stars on GitHub - 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
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
qsea 1.34.0
IP-seq data analysis and vizualization5 versions - Latest release: 3 months ago - 15.4 thousand downloads total - 1 maintainer
TRESS 1.14.0
Toolbox for mRNA epigenetics sequencing analysis5 versions - Latest release: 3 months ago - 1 dependent package - 6.88 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
6 versions - Latest release: 3 months ago - 10 dependent packages - 165 thousand downloads total - 2 maintainers
DSS 2.56.0
Dispersion shrinkage for sequencing data6 versions - Latest release: 3 months ago - 10 dependent packages - 165 thousand downloads total - 2 maintainers
mCSEA 1.28.0
Methylated CpGs Set Enrichment Analysis6 versions - Latest release: 3 months ago - 1 dependent package - 14.2 thousand downloads total - 1 maintainer
ISLET 1.10.0
Individual-Specific ceLl typE referencing Tool5 versions - Latest release: 3 months ago - 5 thousand downloads total - 1 maintainer
dinoR 1.4.0
Differential NOMe-seq analysis3 versions - Latest release: 3 months ago - 3.19 thousand downloads total - 0 stars on GitHub - 1 maintainer
methylInheritance 1.32.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...5 versions - Latest release: 3 months ago - 1 dependent package - 13.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
coMET 1.40.0
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methyl...6 versions - Latest release: 3 months ago - 23.5 thousand downloads total - 1 maintainer
SOMNiBUS 1.16.0
Smooth modeling of bisulfite sequencing6 versions - Latest release: 3 months ago - 5.83 thousand downloads total - 1 stars on GitHub - 1 maintainer
mist 1.0.0
Differential Methylation Analysis for scDNAm Data1 version - Latest release: 3 months ago - 722 downloads total - 0 stars on GitHub - 1 maintainer
COHCAP 1.49.0 removed
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data3 versions - Latest release: about 1 year ago - 20.1 thousand downloads total - 1 maintainer
DMRforPairs 1.38.0 removed
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array bas...2 versions - Latest release: over 1 year ago - 16 thousand downloads total - 1 maintainer
pwrEWAS 1.16.0 removed
A user-friendly tool for comprehensive power estimation for epigenome wide association studies (E...2 versions - Latest release: over 1 year ago - 4.88 thousand downloads total - 1 maintainer
REMP 1.28.0
Repetitive Element Methylation Prediction3 versions - Latest release: about 1 year ago - 12.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
hummingbird 1.14.0
Bayesian Hidden Markov Model for the detection of differentially methylated regions3 versions - Latest release: about 1 year ago - 4.86 thousand downloads total - 1 maintainer
MethCP 1.13.0 removed
Differential methylation anlsysis for bisulfite sequencing data1 version - Latest release: almost 2 years ago - 2.97 thousand downloads total - 4 stars on GitHub - 1 maintainer
exomePeak2 1.14.3 removed
Peak Calling and differential analysis for MeRIP-Seq6 versions - Latest release: over 1 year ago - 8.74 thousand downloads total - 23 stars on GitHub - 1 maintainer
Related Keywords
Software
67
DNAMethylation
48
Sequencing
34
Epigenetics
31
MethylationArray
23
DifferentialExpression
21
GeneExpression
18
ImmunoOncology
17
Microarray
16
Coverage
15
MethylSeq
14
RNASeq
14
QualityControl
13
Regression
12
Preprocessing
12
GeneRegulation
11
DataImport
10
MultipleComparison
10
Normalization
9
Visualization
9
Network
8
TwoChannel
8
StatisticalMethod
7
Transcription
7
Pathways
7
Genetics
7
GeneSetEnrichment
7
BiomedicalInformatics
7
FunctionalGenomics
6
BatchEffect
6
Clustering
5
CopyNumberVariation
5
CpGIsland
5
Transcriptomics
5
SingleCell
5
Bayesian
5
WholeGenome
5
PeakDetection
4
GenomeAnnotation
4
Survival
4
bioconductor
4
r
4
DifferentialPeakCalling
4
CellBiology
4
SystemsBiology
4
ChIPSeq
4
TimeCourse
4
GeneTarget
3
ATACSeq
3
MultiChannel
3
ReportWriting
3
NetworkEnrichment
3
OneChannel
3
HiddenMarkovModel
3
GenomeWideAssociation
3
dna-methylation
2
SNP
2
PrincipalComponent
2
Annotation
2
FunctionalPrediction
2
DifferentialSplicing
2
mRNAMicroarray
2
HistoneModification
2
AlternativeSplicing
2
Classification
2
DNASeq
2
Proteomics
2
FeatureExtraction
2
methylation
2
BiologicalQuestion
2
inheritance
2
GenomicVariation
2
GeneticVariability
2
single-cell
1
methylation-analysis
1
bisulphite-sequencing
1
generalized-linear-models
1
hierarchical-models
1
enrichment
1
ProprietaryPlatforms
1
simulation
1
MicroRNAArray
1
ExonArray
1
TissueMicroarray
1
RiboSeq
1
MotifAnnotation
1
ExomeSeq
1
permutation
1
monte-carlo-sampling
1
differentially-methylated-elements
1
cpg
1
bioinformatics
1
analysis
1
NucleosomePositioning
1
ChipOnChip
1
WorkflowStep
1
differential-methylation
1
ddPCR
1
StructuralVariation
1
RIPSeq
1