bioconductor.org "DNAMethylation" keyword
Top 8.6% on bioconductor.org
7 versions - Latest release: 2 months ago - 2 dependent packages - 46.4 thousand downloads total - 1 maintainer
MethylSeekR 1.52.0
Segmentation of Bis-seq data7 versions - Latest release: 2 months ago - 2 dependent packages - 46.4 thousand downloads total - 1 maintainer
biscuiteer 1.26.0
Convenience Functions for Biscuit7 versions - Latest release: about 1 month ago - 17.7 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
9 versions - Latest release: 2 months ago - 31 dependent packages - 979 thousand downloads total - 64 stars on GitHub - 1 maintainer
minfi 1.58.0
Analyze Illumina Infinium DNA methylation arrays9 versions - Latest release: 2 months ago - 31 dependent packages - 979 thousand downloads total - 64 stars on GitHub - 1 maintainer
les 1.62.0
Identifying Differential Effects in Tiling Microarray Data7 versions - Latest release: 2 months ago - 1 dependent package - 36.4 thousand downloads total - 1 maintainer
pathwayPCA 1.28.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection7 versions - Latest release: about 2 months ago - 1 dependent package - 17.5 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
28 versions - Latest release: about 2 months ago - 181 dependent packages - 4.51 million downloads total - 4 maintainers
edgeR 4.10.1
Empirical Analysis of Digital Gene Expression Data in R28 versions - Latest release: about 2 months ago - 181 dependent packages - 4.51 million downloads total - 4 maintainers
mitch 1.24.0
Multi-Contrast Gene Set Enrichment Analysis10 versions - Latest release: 2 months ago - 16.7 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
7 versions - Latest release: 2 months ago - 10 dependent packages - 417 thousand downloads total - 1 maintainer
lumi 2.64.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays7 versions - Latest release: 2 months ago - 10 dependent packages - 417 thousand downloads total - 1 maintainer
GEM 1.38.0
GEM: fast association study for the interplay of Gene, Environment and Methylation7 versions - Latest release: about 1 month ago - 18.4 thousand downloads total - 1 maintainer
RBedMethyl 1.0.0
Disk-backed Representation of ONT bedMethyl Files1 version - Latest release: 2 months ago - 1.05 thousand downloads total - 1 maintainer
Moonlight2R 1.10.1
Identify oncogenes and tumor suppressor genes from omics data9 versions - Latest release: 3 days ago - 8.27 thousand downloads total - 5 stars on GitHub - 1 maintainer
CTexploreR 1.8.0
Explores Cancer Testis Genes5 versions - Latest release: about 2 months ago - 6.87 thousand downloads total - 0 stars on GitHub - 1 maintainer
methInheritSim 1.34.0
Simulating Whole-Genome Inherited Bisulphite Sequencing Data7 versions - Latest release: about 1 month ago - 1 dependent package - 18.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
recountmethylation 1.22.0
Access and analyze public DNA methylation array data compilations7 versions - Latest release: about 1 month ago - 13.6 thousand downloads total - 8 stars on GitHub - 1 maintainer
methrix 1.26.0
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing8 versions - Latest release: 2 months ago - 1 dependent package - 19.8 thousand downloads total - 36 stars on GitHub - 1 maintainer
MIRA 1.34.0
Methylation-Based Inference of Regulatory Activity7 versions - Latest release: 2 months ago - 1 dependent package - 20.7 thousand downloads total - 1 maintainer
knowYourCG 1.8.0
Functional analysis of DNA methylome datasets8 versions - Latest release: about 1 month ago - 7 stars on GitHub - 1 maintainer
methylscaper 1.20.0
Visualization of Methylation Data8 versions - Latest release: about 1 month ago - 1 stars on GitHub - 1 maintainer
mist 1.4.0
Differential Methylation Analysis for scDNAm Data4 versions - Latest release: about 1 month ago - 1 stars on GitHub - 1 maintainer
epimutacions 1.16.0
Robust outlier identification for DNA methylation data8 versions - Latest release: 2 months ago - 0 stars on GitHub - 1 maintainer
vmrseq 1.4.0
Probabilistic Modeling of Single-cell Methylation Heterogeneity4 versions - Latest release: about 2 months ago - 9 stars on GitHub - 1 maintainer
Top 10.0% on bioconductor.org
7 versions - Latest release: about 2 months ago - 2 dependent packages - 54 stars on GitHub - 1 maintainer
EpiDISH 2.28.0
Epigenetic Dissection of Intra-Sample-Heterogeneity7 versions - Latest release: about 2 months ago - 2 dependent packages - 54 stars on GitHub - 1 maintainer
TurboNorm 1.60.0
A fast scatterplot smoother suitable for microarray normalization7 versions - Latest release: about 1 month ago - 1 maintainer
decemedip 1.0.0
hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methy...1 version - Latest release: 2 months ago - 4 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: 2 months ago - 7 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
7 versions - Latest release: 2 months ago - 1 maintainer
MEDIPS 1.64.0
DNA IP-seq data analysis7 versions - Latest release: 2 months ago - 1 maintainer
mCSEA 1.32.0
Methylated CpGs Set Enrichment Analysis9 versions - Latest release: about 2 months ago - 1 dependent package - 1 maintainer
Top 3.3% on bioconductor.org
8 versions - Latest release: about 1 month ago - 5 dependent packages - 4 maintainers
missMethyl 1.46.0
Analysing Illumina HumanMethylation BeadChip Data8 versions - Latest release: about 1 month ago - 5 dependent packages - 4 maintainers
Top 3.7% on bioconductor.org
8 versions - Latest release: about 2 months ago - 12 dependent packages - 38 stars on GitHub - 1 maintainer
bsseq 1.48.0
Analyze, manage and store whole-genome methylation data8 versions - Latest release: about 2 months ago - 12 dependent packages - 38 stars on GitHub - 1 maintainer
methylPipe 1.46.0
Base resolution DNA methylation data analysis8 versions - Latest release: about 2 months ago - 1 dependent package - 1 maintainer
methylCC 1.26.0
Estimate the cell composition of whole blood in DNA methylation samples8 versions - Latest release: 2 months ago - 18 stars on GitHub - 1 maintainer
methylGSA 1.30.0
Gene Set Analysis Using the Outcome of Differential Methylation7 versions - Latest release: about 2 months ago - 13 stars on GitHub - 1 maintainer
scMET 1.14.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity7 versions - Latest release: about 2 months ago - 18 stars on GitHub - 1 maintainer
MEAT 1.24.0
Muscle Epigenetic Age Test7 versions - Latest release: about 2 months ago - 1 stars on GitHub - 1 maintainer
SingleMoleculeFootprinting 2.5.0
Analysis tools for Single Molecule Footprinting (SMF) data7 versions - Latest release: about 2 months ago - 2 stars on GitHub - 1 maintainer
methylclock 1.18.0
Methylclock - DNA methylation-based clocks7 versions - Latest release: about 2 months ago - 53 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
7 versions - Latest release: 2 months ago - 1 dependent package - 51 stars on GitHub - 1 maintainer
RTCGA 1.41.0
The Cancer Genome Atlas Data Integration7 versions - Latest release: 2 months ago - 1 dependent package - 51 stars on GitHub - 1 maintainer
PoDCall 1.20.0
Positive Droplet Calling for DNA Methylation Droplet Digital PCR8 versions - Latest release: about 2 months ago - 1 maintainer
COCOA 2.26.0
Coordinate Covariation Analysis7 versions - Latest release: about 2 months ago - 1 maintainer
Top 4.7% on bioconductor.org
7 versions - Latest release: about 2 months ago - 1 dependent package - 1 maintainer
RnBeads 2.30.0
RnBeads7 versions - Latest release: about 2 months ago - 1 dependent package - 1 maintainer
ramwas 1.36.0
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms7 versions - Latest release: 2 months ago - 1 maintainer
qsea 1.38.0
IP-seq data analysis and vizualization7 versions - Latest release: 17 days ago - 1 maintainer
skewr 1.44.0
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip7 versions - Latest release: 2 months ago - 1 maintainer
epialleleR 1.20.0
Fast, Accurate, Epiallele-Aware Methylation Caller and Reporter7 versions - Latest release: 2 months ago - 6 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
7 versions - Latest release: about 2 months ago - 15 dependent packages - 18 stars on GitHub - 1 maintainer
bumphunter 1.54.0
Bump Hunter7 versions - Latest release: about 2 months ago - 15 dependent packages - 18 stars on GitHub - 1 maintainer
betaHMM 1.8.0
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Be...7 versions - Latest release: about 2 months ago - 1 maintainer
MethPed 1.40.0
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes7 versions - Latest release: about 2 months ago - 1 maintainer
dmrseq 1.32.0
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing10 versions - Latest release: about 2 months ago - 1 dependent package - 1 maintainer
Top 9.5% on bioconductor.org
8 versions - Latest release: about 2 months ago - 1 maintainer
BiSeq 1.52.0
Processing and analyzing bisulfite sequencing data8 versions - Latest release: about 2 months ago - 1 maintainer
TOAST 1.26.0
Tools for the analysis of heterogeneous tissues7 versions - Latest release: about 2 months ago - 3 dependent packages - 8 stars on GitHub - 1 maintainer
deconvR 1.18.0
Simulation and Deconvolution of Omic Profiles8 versions - Latest release: about 2 months ago - 9 stars on GitHub - 1 maintainer
borealis 1.16.0
Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution7 versions - Latest release: about 2 months ago - 1 maintainer
DMRcaller 1.44.0
Differentially Methylated Regions Caller7 versions - Latest release: about 2 months ago - 1 maintainer
GAprediction 1.38.0
Prediction of gestational age with Illumina HumanMethylation450 data7 versions - Latest release: 2 months ago - 1 maintainer
methylInheritance 1.36.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...8 versions - Latest release: about 2 months ago - 1 dependent package - 0 stars on GitHub - 1 maintainer
MethylAid 1.46.0
Visual and interactive quality control of large Illumina DNA Methylation array data sets7 versions - Latest release: about 2 months ago - 1 maintainer
methimpute 1.34.0
Imputation-guided re-construction of complete methylomes from WGBS data7 versions - Latest release: about 2 months ago - 1 maintainer
Top 9.3% on bioconductor.org
7 versions - Latest release: about 2 months ago - 1 maintainer
HELP 1.70.0
Tools for HELP data analysis7 versions - Latest release: about 2 months ago - 1 maintainer
ARRmNormalization 1.52.0
Adaptive Robust Regression normalization for Illumina methylation data7 versions - Latest release: about 2 months ago - 1 maintainer
Top 7.4% on bioconductor.org
8 versions - Latest release: 2 months ago - 1 maintainer
ELMER 2.35.1
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes8 versions - Latest release: 2 months ago - 1 maintainer
conumee 1.46.0
Enhanced copy-number variation analysis using Illumina DNA methylation arrays7 versions - Latest release: 2 months ago - 1 maintainer
iCheck 1.42.0
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data7 versions - Latest release: 2 months ago - 1 maintainer
EpiMix 1.14.0
EpiMix: an integrative tool for the population-level analysis of DNA methylation7 versions - Latest release: about 2 months ago - 1 dependent package - 1 stars on GitHub - 1 maintainer
HIREewas 1.30.0
Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies7 versions - Latest release: 2 months ago - 1 maintainer
Top 3.8% on bioconductor.org
8 versions - Latest release: about 2 months ago - 3 dependent packages - 247 stars on GitHub - 2 maintainers
methylKit 1.38.0
DNA methylation analysis from high-throughput bisulfite sequencing results8 versions - Latest release: about 2 months ago - 3 dependent packages - 247 stars on GitHub - 2 maintainers
EnMCB 1.24.0
Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models7 versions - Latest release: about 2 months ago - 9 stars on GitHub - 1 maintainer
NanoMethViz 3.8.0
Visualise methylation data from Oxford Nanopore sequencing7 versions - Latest release: 2 months ago - 32 stars on GitHub - 1 maintainer
Lheuristic 1.4.0
Detection of scatterplots with L-shaped pattern3 versions - Latest release: 2 months ago - 0 stars on GitHub - 1 maintainer
Top 8.9% on bioconductor.org
7 versions - Latest release: 2 months ago - 1 maintainer
MEDME 1.72.0
Modelling Experimental Data from MeDIP Enrichment7 versions - Latest release: 2 months ago - 1 maintainer
BEAT 1.50.0
BEAT - BS-Seq Epimutation Analysis Toolkit7 versions - Latest release: 2 months ago - 1 maintainer
funtooNorm 1.36.0
Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit7 versions - Latest release: 2 months ago - 1 maintainer
methyLImp2 1.8.0
Missing value estimation of DNA methylation data5 versions - Latest release: 2 months ago - 4 stars on GitHub - 1 maintainer
iNETgrate 1.10.0
Integrates DNA methylation data with gene expression in a single gene network7 versions - Latest release: 2 months ago - 6.87 thousand downloads total - 65 stars on GitHub - 1 maintainer
ENmix 1.48.0
Quality control and analysis tools for Illumina DNA methylation BeadChip13 versions - Latest release: 2 months ago - 51.4 thousand downloads total - 1 maintainer
methodical 1.8.0
Discovering genomic regions where methylation is strongly associated with transcriptional activity6 versions - Latest release: about 2 months ago - 0 stars on GitHub - 1 maintainer
ramr 1.20.0
Detection of Rare Aberrantly Methylated Regions in Array and NGS Data7 versions - Latest release: 2 months ago - 0 stars on GitHub - 1 maintainer
methylMnM 1.50.0
detect different methylation level (DMR)7 versions - Latest release: about 2 months ago - 1 dependent package - 27.2 thousand downloads total
scmeth 1.32.0
Functions to conduct quality control analysis in methylation data7 versions - Latest release: 2 months ago - 1 dependent package - 17.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.2% on bioconductor.org
8 versions - Latest release: 2 months ago - 10 dependent packages - 206 thousand downloads total - 2 maintainers
DSS 2.60.0
Dispersion shrinkage for sequencing data8 versions - Latest release: 2 months ago - 10 dependent packages - 206 thousand downloads total - 2 maintainers
planet 1.20.0
Placental DNA methylation analysis tools7 versions - Latest release: 2 months ago - 1 dependent package - 18 thousand downloads total - 4 stars on GitHub - 1 maintainer
SOMNiBUS 1.20.0
Smooth modeling of bisulfite sequencing8 versions - Latest release: 27 days ago - 9.54 thousand downloads total - 1 stars on GitHub - 1 maintainer
Harman 1.40.0
The removal of batch effects from datasets using a PCA and constrained optimisation based technique7 versions - Latest release: 2 months ago - 1 dependent package - 33.4 thousand downloads total - 1 maintainer
dmGsea 1.2.1
Efficient Gene Set Enrichment Analysis for DNA Methylation Data5 versions - Latest release: 28 days ago - 3.35 thousand downloads total - 1 maintainer
shinyepico 1.20.0
ShinyÉPICo7 versions - Latest release: about 2 months ago - 11.6 thousand downloads total - 5 stars on GitHub - 1 maintainer
Melissa 1.28.0
Bayesian clustering and imputationa of single cell methylomes9 versions - Latest release: 28 days ago - 12.1 thousand downloads total - 1 maintainer
normalize450K 1.40.0
Preprocessing of Illumina Infinium 450K data7 versions - Latest release: 28 days ago - 18.2 thousand downloads total - 1 maintainer
BPRMeth 1.38.0
Model higher-order methylation profiles7 versions - Latest release: 2 months ago - 1 dependent package - 22.7 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
7 versions - Latest release: 29 days ago - 34.7 thousand downloads total - 1 maintainer
MassArray 1.64.0
Analytical Tools for MassArray Data7 versions - Latest release: 29 days ago - 34.7 thousand downloads total - 1 maintainer
bigmelon 1.38.0
Illumina methylation array analysis for large experiments7 versions - Latest release: 2 months ago - 24.4 thousand downloads total - 1 maintainer
TransView 1.54.0 removed
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets8 versions - Latest release: 5 months ago - 29.7 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
8 versions - Latest release: 2 months ago - 1 dependent package - 164 thousand downloads total - 1 maintainer
ChAMP 2.42.0
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC8 versions - Latest release: 2 months ago - 1 dependent package - 164 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
7 versions - Latest release: 2 months ago - 5 dependent packages - 189 thousand downloads total - 1 maintainer
wateRmelon 2.18.0
Illumina DNA methylation array normalization and metrics7 versions - Latest release: 2 months ago - 5 dependent packages - 189 thousand downloads total - 1 maintainer
MAGAR 1.20.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...7 versions - Latest release: 2 months ago - 12.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
DAMEfinder 1.24.0
Finds DAMEs - Differential Allelicly MEthylated regions7 versions - Latest release: 2 months ago - 16.4 thousand downloads total - 9 stars on GitHub - 1 maintainer
iscream 1.2.0
Make fast and memory efficient BED file queries, summaries and matrices2 versions - Latest release: about 1 month ago - 1.96 thousand downloads total - 0 stars on GitHub - 1 maintainer
MPFE 1.48.0
Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data7 versions - Latest release: 2 months ago - 19.8 thousand downloads total - 1 maintainer
BEclear 2.28.0
Correction of batch effects in DNA methylation data7 versions - Latest release: about 1 month ago - 25.8 thousand downloads total - 5 stars on GitHub - 1 maintainer
GeoTcgaData 2.12.0
Processing Various Types of Data on GEO and TCGA7 versions - Latest release: 2 months ago - 10.3 thousand downloads total - 28 stars on GitHub - 1 maintainer
Top 5.6% on bioconductor.org
10 versions - Latest release: 2 months ago - 4 dependent packages - 97.1 thousand downloads total - 80 stars on GitHub - 1 maintainer
sesame 1.30.0
SEnsible Step-wise Analysis of DNA MEthylation BeadChips10 versions - Latest release: 2 months ago - 4 dependent packages - 97.1 thousand downloads total - 80 stars on GitHub - 1 maintainer
Related Keywords
Software
126
Epigenetics
51
DifferentialMethylation
49
Sequencing
44
MethylationArray
42
Microarray
39
Preprocessing
34
GeneExpression
30
ImmunoOncology
30
MethylSeq
26
QualityControl
26
TwoChannel
20
Normalization
18
DataImport
18
DifferentialExpression
17
Coverage
17
Regression
15
Genetics
15
GeneRegulation
14
CpGIsland
13
Visualization
13
Transcription
12
SingleCell
12
RNASeq
11
StatisticalMethod
10
MultipleComparison
10
CopyNumberVariation
9
BiomedicalInformatics
9
Transcriptomics
9
Network
8
dna-methylation
8
GeneSetEnrichment
8
Clustering
8
Pathways
8
BatchEffect
8
WholeGenome
8
ChIPSeq
7
PrincipalComponent
7
FunctionalGenomics
7
Survival
7
GenomeAnnotation
6
Bayesian
6
methylation
6
GenomeWideAssociation
6
SystemsBiology
6
SNP
6
OneChannel
5
bioconductor
5
FeatureExtraction
5
BiologicalQuestion
4
GenomicVariation
4
GeneticVariability
4
bioinformatics
4
GeneTarget
4
Classification
4
Proteomics
4
CellBiology
3
DataRepresentation
3
r
3
HiddenMarkovModel
3
KEGG
3
MultiChannel
3
bioconductor-package
3
Spatial
2
NucleosomePositioning
2
omics
2
next-generation-sequencing
2
LongRead
2
dna-methylation-data
2
r-package
2
bayesian-inference
2
ATACSeq
2
Annotation
2
GenePrediction
2
MotifAnnotation
2
DimensionReduction
2
TimeCourse
2
GraphAndNetwork
2
GUI
2
Infrastructure
2
NetworkEnrichment
2
mRNAMicroarray
2
inheritance
2
inference
1
machine-learning
1
epigenetics
1
ancestry
1
genetics
1
placenta
1
FunctionalPrediction
1
TissueMicroarray
1
single-cell-methylation
1
methylation-microarrays
1
epimutation
1
aberrant-methylation
1
cran
1
core-services
1
NetworkInference
1
missing-value-imputation
1
imputation
1