bioconductor.org "DifferentialMethylation" keyword
View the packages on the bioconductor.org package registry that are tagged with the "DifferentialMethylation" keyword.
Top 1.9% on bioconductor.org
8 versions - Latest release: 2 months ago - 31 dependent packages - 930 thousand downloads total - 64 stars on GitHub - 1 maintainer
minfi 1.56.0
Analyze Illumina Infinium DNA methylation arrays8 versions - Latest release: 2 months ago - 31 dependent packages - 930 thousand downloads total - 64 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
26 versions - Latest release: 8 days ago - 181 dependent packages - 4.18 million downloads total - 4 maintainers
edgeR 4.8.2
Empirical Analysis of Digital Gene Expression Data in R26 versions - Latest release: 8 days ago - 181 dependent packages - 4.18 million downloads total - 4 maintainers
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
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
Top 3.3% on bioconductor.org
7 versions - Latest release: about 1 month ago - 5 dependent packages - 180 thousand downloads total - 4 maintainers
missMethyl 1.44.0
Analysing Illumina HumanMethylation BeadChip Data7 versions - Latest release: about 1 month ago - 5 dependent packages - 180 thousand downloads total - 4 maintainers
shinyepico 1.18.0
ShinyÉPICo6 versions - Latest release: about 1 month ago - 9.09 thousand downloads total - 5 stars on GitHub - 1 maintainer
DMCFB 1.24.0
Differentially Methylated Cytosines via a Bayesian Functional Approach8 versions - Latest release: about 1 month ago - 10.3 thousand 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
ramwas 1.34.0
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms6 versions - Latest release: about 1 month ago - 20 thousand downloads total - 1 maintainer
ramr 1.18.0
Detection of Rare Aberrantly Methylated Regions in Array and NGS Data6 versions - Latest release: about 1 month ago - 9.2 thousand downloads total - 0 stars on GitHub - 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
HIREewas 1.28.0
Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies6 versions - Latest release: about 1 month ago - 11.6 thousand downloads total - 1 maintainer
betaHMM 1.6.0
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Be...6 versions - Latest release: about 1 month ago - 4.74 thousand downloads total - 1 maintainer
DMCHMM 1.32.0
Differentially Methylated CpG using Hidden Markov Model6 versions - Latest release: about 1 month ago - 14.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
mCSEA 1.30.1
Methylated CpGs Set Enrichment Analysis8 versions - Latest release: 10 days ago - 1 dependent package - 16.5 thousand downloads total - 1 maintainer
PoDCall 1.18.0
Positive Droplet Calling for DNA Methylation Droplet Digital PCR7 versions - Latest release: about 1 month ago - 7.12 thousand downloads total - 1 maintainer
TRESS 1.16.0
Toolbox for mRNA epigenetics sequencing analysis6 versions - Latest release: about 1 month ago - 1 dependent package - 9.04 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
cfTools 1.10.0
Informatics Tools for Cell-Free DNA Study6 versions - Latest release: about 1 month ago - 5.81 thousand downloads total - 6 stars on GitHub - 1 maintainer
NanoMethViz 3.6.0
Visualise methylation data from Oxford Nanopore sequencing6 versions - Latest release: about 1 month ago - 12.6 thousand downloads total - 32 stars on GitHub - 1 maintainer
dmrseq 1.30.0
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing9 versions - Latest release: about 1 month ago - 1 dependent package - 33.3 thousand downloads total - 1 maintainer
borealis 1.14.0
Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution6 versions - Latest release: about 1 month ago - 6.76 thousand downloads total - 1 maintainer
DAMEfinder 1.22.0
Finds DAMEs - Differential Allelicly MEthylated regions6 versions - Latest release: about 1 month ago - 13.3 thousand downloads total - 9 stars on GitHub - 1 maintainer
IWTomics 1.33.0
Interval-Wise Testing for Omics Data6 versions - Latest release: about 1 month ago - 16.8 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
MAGAR 1.18.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...6 versions - Latest release: about 1 month ago - 9.73 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.2% on bioconductor.org
7 versions - Latest release: about 1 month ago - 10 dependent packages - 195 thousand downloads total - 2 maintainers
DSS 2.58.0
Dispersion shrinkage for sequencing data7 versions - Latest release: about 1 month ago - 10 dependent packages - 195 thousand downloads total - 2 maintainers
dinoR 1.6.0
Differential NOMe-seq analysis4 versions - Latest release: about 1 month ago - 4.59 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
6 versions - Latest release: about 1 month ago - 1 dependent package - 78.7 thousand downloads total - 1 maintainer
RnBeads 2.28.0
RnBeads6 versions - Latest release: about 1 month ago - 1 dependent package - 78.7 thousand downloads total - 1 maintainer
Top 8.7% on bioconductor.org
6 versions - Latest release: about 1 month ago - 1 dependent package - 36.1 thousand downloads total - 10 stars on GitHub - 1 maintainer
regionReport 1.44.0
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results6 versions - Latest release: about 1 month ago - 1 dependent package - 36.1 thousand downloads total - 10 stars on GitHub - 1 maintainer
SOMNiBUS 1.18.0
Smooth modeling of bisulfite sequencing7 versions - Latest release: about 1 month ago - 7.29 thousand downloads total - 1 stars on GitHub - 1 maintainer
magpie 1.10.0
MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation6 versions - Latest release: about 1 month ago - 5.92 thousand downloads total - 0 stars on GitHub - 1 maintainer
msgbsR 1.34.0
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions6 versions - Latest release: about 2 months ago - 15.1 thousand downloads total - 1 maintainer
methInheritSim 1.32.0
Simulating Whole-Genome Inherited Bisulphite Sequencing Data6 versions - Latest release: about 2 months ago - 1 dependent package - 14.6 thousand downloads total - 2 stars on GitHub - 1 maintainer
ISLET 1.12.0
Individual-Specific ceLl typE referencing Tool6 versions - Latest release: about 2 months ago - 6.62 thousand downloads total - 1 maintainer
TOAST 1.24.0
Tools for the analysis of heterogeneous tissues6 versions - Latest release: about 2 months ago - 3 dependent packages - 34.1 thousand downloads total - 8 stars on GitHub - 1 maintainer
spiky 1.16.0
Spike-in calibration for cell-free MeDIP6 versions - Latest release: about 2 months ago - 7.67 thousand downloads total - 3 stars on GitHub - 1 maintainer
Damsel 1.6.0
Damsel: an end to end analysis of DamID5 versions - Latest release: about 1 month ago - 4.12 thousand downloads total - 0 stars on GitHub - 1 maintainer
SMITE 1.38.0
Significance-based Modules Integrating the Transcriptome and Epigenome6 versions - Latest release: about 1 month ago - 18.1 thousand downloads total - 1 stars on GitHub - 2 maintainers
Top 10.0% on bioconductor.org
6 versions - Latest release: about 2 months ago - 2 dependent packages - 53.5 thousand downloads total - 54 stars on GitHub - 1 maintainer
EpiDISH 2.26.0
Epigenetic Dissection of Intra-Sample-Heterogeneity6 versions - Latest release: about 2 months ago - 2 dependent packages - 53.5 thousand downloads total - 54 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
EpiMix 1.12.0
EpiMix: an integrative tool for the population-level analysis of DNA methylation6 versions - Latest release: about 2 months ago - 1 dependent package - 6.63 thousand downloads total - 1 stars on GitHub - 1 maintainer
regionalpcs 1.7.0
Summarizing Regional Methylation with Regional Principal Components Analysis5 versions - Latest release: about 2 months ago - 5.15 thousand downloads total - 3 stars on GitHub - 1 maintainer
mist 1.2.0
Differential Methylation Analysis for scDNAm Data2 versions - Latest release: about 2 months ago - 1.95 thousand downloads total - 1 stars on GitHub - 1 maintainer
ENmix 1.46.0
Quality control and analysis tools for Illumina DNA methylation BeadChip10 versions - Latest release: about 2 months ago - 46.8 thousand downloads total - 1 maintainer
GeoTcgaData 2.10.0
Processing Various Types of Data on GEO and TCGA6 versions - Latest release: about 2 months ago - 7.97 thousand downloads total - 28 stars on GitHub - 1 maintainer
SIMD 1.28.0
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site6 versions - Latest release: about 2 months ago - 11 thousand downloads total - 1 maintainer
coMethDMR 1.14.0
Accurate identification of co-methylated and differentially methylated regions in epigenome-wide ...6 versions - Latest release: about 2 months ago - 7.65 thousand downloads total - 7 stars on GitHub - 1 maintainer
planet 1.18.0
Placental DNA methylation analysis tools6 versions - Latest release: about 2 months ago - 1 dependent package - 14.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
methylSig 1.22.0
MethylSig: Differential Methylation Testing for WGBS and RRBS Data6 versions - Latest release: about 2 months ago - 12.8 thousand downloads total - 15 stars on GitHub - 1 maintainer
AMARETTO 1.26.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...6 versions - Latest release: about 2 months ago - 16.4 thousand downloads total - 1 maintainer
qsea 1.36.0
IP-seq data analysis and vizualization6 versions - Latest release: about 2 months ago - 17.3 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
8 versions - Latest release: about 2 months ago - 7 dependent packages - 550 thousand downloads total - 339 stars on GitHub - 2 maintainers
TCGAbiolinks 2.38.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data8 versions - Latest release: about 2 months ago - 7 dependent packages - 550 thousand downloads total - 339 stars on GitHub - 2 maintainers
Moonlight2R 1.8.0
Identify oncogenes and tumor suppressor genes from omics data6 versions - Latest release: 25 days ago - 5.56 thousand downloads total - 5 stars on GitHub - 1 maintainer
DMRcaller 1.42.0
Differentially Methylated Regions Caller6 versions - Latest release: 2 months ago - 25.2 thousand downloads total - 1 maintainer
omicRexposome 1.32.0
Exposome and omic data associatin and integration analysis7 versions - Latest release: 2 months ago - 14.3 thousand downloads total - 1 maintainer
nempi 1.18.0
Inferring unobserved perturbations from gene expression data6 versions - Latest release: about 1 month ago - 7.82 thousand downloads total - 2 stars on GitHub - 1 maintainer
coMET 1.40.0 removed
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methyl...6 versions - Latest release: 9 months ago - 24.4 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
14 versions - Latest release: about 1 month ago - 2 dependent packages - 188 thousand downloads total - 1 maintainer
DMRcate 3.6.0
Methylation array and sequencing spatial analysis methods14 versions - Latest release: about 1 month ago - 2 dependent packages - 188 thousand downloads total - 1 maintainer
methylInheritance 1.34.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...7 versions - Latest release: about 1 month ago - 1 dependent package - 15.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
MethCP 1.13.0 removed
Differential methylation anlsysis for bisulfite sequencing data1 version - Latest release: about 2 years ago - 2.97 thousand downloads total - 4 stars on GitHub - 1 maintainer
REMP 1.28.0
Repetitive Element Methylation Prediction3 versions - Latest release: over 1 year ago - 12.8 thousand downloads total - 3 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: over 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: about 2 years 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: about 2 years ago - 4.88 thousand downloads total - 1 maintainer
hummingbird 1.14.0
Bayesian Hidden Markov Model for the detection of differentially methylated regions3 versions - Latest release: over 1 year ago - 4.86 thousand downloads total - 1 maintainer
exomePeak2 1.14.3 removed
Peak Calling and differential analysis for MeRIP-Seq6 versions - Latest release: about 2 years 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
RNASeq
14
MethylSeq
14
QualityControl
13
Regression
12
Preprocessing
12
GeneRegulation
11
DataImport
10
MultipleComparison
10
Normalization
9
Visualization
9
Network
8
TwoChannel
8
StatisticalMethod
7
GeneSetEnrichment
7
Genetics
7
BiomedicalInformatics
7
Pathways
7
Transcription
7
FunctionalGenomics
6
BatchEffect
6
WholeGenome
5
CopyNumberVariation
5
CpGIsland
5
Transcriptomics
5
SingleCell
5
Bayesian
5
Clustering
5
bioconductor
4
GenomeAnnotation
4
CellBiology
4
ChIPSeq
4
Survival
4
r
4
PeakDetection
4
SystemsBiology
4
TimeCourse
4
DifferentialPeakCalling
4
GeneTarget
3
HiddenMarkovModel
3
MultiChannel
3
ATACSeq
3
NetworkEnrichment
3
OneChannel
3
ReportWriting
3
GenomeWideAssociation
3
SNP
2
inheritance
2
mRNAMicroarray
2
FunctionalPrediction
2
methylation
2
Annotation
2
DNASeq
2
Classification
2
BiologicalQuestion
2
DifferentialSplicing
2
Proteomics
2
dna-methylation
2
PrincipalComponent
2
GeneticVariability
2
GenomicVariation
2
AlternativeSplicing
2
FeatureExtraction
2
HistoneModification
2
TissueMicroarray
1
integrative-analysis
1
gdc
1
bioc
1
ChipOnChip
1
ProprietaryPlatforms
1
MicroRNAArray
1
ExonArray
1
differential-methylation
1
placenta
1
machine-learning
1
inference
1
genetics
1
epigenetics
1
dna-methylation-data
1
ancestry
1
permutation
1
monte-carlo-sampling
1
differentially-methylated-elements
1
cpg
1
bioinformatics
1
analysis
1
RiboSeq
1
MotifAnnotation
1
ExomeSeq
1
PooledScreens
1
NeuralNetwork
1