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bioconductor.org "DNAMethylation" keyword

MethPed 1.40.0
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
7 versions - Latest release: 5 months ago - 26.7 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.64.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
7 versions - Latest release: 5 months ago - 10 dependent packages - 436 thousand downloads total - 1 maintainer
omicsPrint 1.32.0
Cross omic genetic fingerprinting
7 versions - Latest release: 4 months ago - 23.7 thousand downloads total - 1 maintainer
methimpute 1.34.0
Imputation-guided re-construction of complete methylomes from WGBS data
7 versions - Latest release: 5 months ago - 24.8 thousand downloads total - 1 maintainer
MEAL 1.42.0
Perform methylation analysis
7 versions - Latest release: 5 months ago - 33 thousand downloads total - 1 maintainer
vmrseq 1.4.0
Probabilistic Modeling of Single-cell Methylation Heterogeneity
4 versions - Latest release: 4 months ago - 6.32 thousand downloads total - 11 stars on GitHub - 1 maintainer
mist 1.4.0
Differential Methylation Analysis for scDNAm Data
4 versions - Latest release: 4 months ago - 6.53 thousand downloads total - 2 stars on GitHub - 1 maintainer
Lheuristic 1.4.0
Detection of scatterplots with L-shaped pattern
3 versions - Latest release: 5 months ago - 5.25 thousand downloads total - 0 stars on GitHub - 1 maintainer
HIREewas 1.30.0
Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies
7 versions - Latest release: 5 months ago - 15.6 thousand downloads total - 1 maintainer
RBedMethyl 1.0.0
Disk-backed Representation of ONT bedMethyl Files
1 version - Latest release: 5 months ago - 3.36 thousand downloads total - 0 stars on GitHub - 1 maintainer
qsea 1.38.0
IP-seq data analysis and vizualization
7 versions - Latest release: 3 months ago - 27.2 thousand downloads total - 1 maintainer
skewr 1.44.0
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
7 versions - Latest release: 5 months ago - 26.1 thousand downloads total - 1 maintainer
methrix 1.26.0
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing
8 versions - Latest release: 5 months ago - 1 dependent package - 23.6 thousand downloads total - 36 stars on GitHub - 1 maintainer
biscuiteer 1.26.0
Convenience Functions for Biscuit
7 versions - Latest release: 4 months ago - 22.2 thousand downloads total - 6 stars on GitHub - 1 maintainer
shinyMethyl 1.48.0
Interactive visualization for Illumina methylation arrays
7 versions - Latest release: 5 months ago - 43.2 thousand downloads total - 6 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 - 2 stars on GitHub - 1 maintainer
MoonlightR 1.38.0
Identify oncogenes and tumor suppressor genes from omics data
7 versions - Latest release: 4 months ago - 26.3 thousand downloads total - 17 stars on GitHub - 1 maintainer
methodical 1.8.0
Discovering genomic regions where methylation is strongly associated with transcriptional activity
6 versions - Latest release: 5 months ago - 13 thousand downloads total - 0 stars on GitHub - 1 maintainer
shinyepico 1.20.0
ShinyÉPICo
7 versions - Latest release: 5 months ago - 16.3 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.58.0
Analyze Illumina Infinium DNA methylation arrays
9 versions - Latest release: 5 months ago - 31 dependent packages - 1.01 million downloads total - 64 stars on GitHub - 1 maintainer
methInheritSim 1.34.0
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
7 versions - Latest release: 4 months ago - 1 dependent package - 22.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
NanoMethViz 3.8.0
Visualise methylation data from Oxford Nanopore sequencing
7 versions - Latest release: 5 months ago - 19.8 thousand downloads total - 37 stars on GitHub - 1 maintainer
Top 9.3% on bioconductor.org
HELP 1.70.0
Tools for HELP data analysis
7 versions - Latest release: 5 months ago - 45.3 thousand downloads total - 1 maintainer
Top 3.7% on bioconductor.org
bsseq 1.48.0
Analyze, manage and store whole-genome methylation data
8 versions - Latest release: 4 months ago - 12 dependent packages - 311 thousand downloads total - 38 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
ChAMP 2.42.0
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
8 versions - Latest release: 5 months ago - 1 dependent package - 171 thousand downloads total - 1 maintainer
methylGSA 1.30.0
Gene Set Analysis Using the Outcome of Differential Methylation
7 versions - Latest release: 4 months ago - 26.9 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.10.5
Empirical Analysis of Digital Gene Expression Data in R
30 versions - Latest release: 25 days ago - 181 dependent packages - 4.79 million downloads total - 4 maintainers
Top 8.9% on bioconductor.org
MEDME 1.72.0
Modelling Experimental Data from MeDIP Enrichment
7 versions - Latest release: 5 months ago - 44 thousand downloads total - 1 maintainer
MBAmethyl 1.46.0
Model-based analysis of DNA methylation data
7 versions - Latest release: 4 months ago - 21.7 thousand downloads total - 1 maintainer
ENmix 1.48.3
Quality control and analysis tools for Illumina DNA methylation BeadChip
14 versions - Latest release: 3 months ago - 57.7 thousand downloads total - 1 maintainer
CTexploreR 1.8.0
Explores Cancer Testis Genes
5 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 sequencing
8 versions - Latest release: 4 months ago - 12.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
dmGsea 1.2.2
Efficient Gene Set Enrichment Analysis for DNA Methylation Data
6 versions - Latest release: about 2 months ago - 6.69 thousand downloads total - 1 maintainer
dmrseq 1.32.0
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
10 versions - Latest release: 5 months ago - 1 dependent package - 42.1 thousand downloads total - 1 maintainer
Moonlight2R 1.10.1
Identify oncogenes and tumor suppressor genes from omics data
9 versions - Latest release: 3 months ago - 12.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
normalize450K 1.40.0
Preprocessing of Illumina Infinium 450K data
7 versions - Latest release: 4 months ago - 22.7 thousand downloads total - 1 maintainer
BEAT 1.50.0
BEAT - BS-Seq Epimutation Analysis Toolkit
7 versions - Latest release: 5 months ago - 33.3 thousand downloads total - 1 maintainer
methylInheritance 1.36.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...
8 versions - Latest release: 5 months ago - 1 dependent package - 23.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
spiky 1.18.0
Spike-in calibration for cell-free MeDIP
7 versions - Latest release: 4 months ago - 12.9 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
RTCGA 1.41.0
The Cancer Genome Atlas Data Integration
7 versions - Latest release: 5 months ago - 1 dependent package - 106 thousand downloads total - 51 stars on GitHub - 1 maintainer
regionalpcs 1.10.0
Summarizing Regional Methylation with Regional Principal Components Analysis
7 versions - Latest release: 4 months ago - 9.68 thousand downloads total - 4 stars on GitHub - 1 maintainer
planet 1.20.0
Placental DNA methylation analysis tools
7 versions - Latest release: 5 months ago - 1 dependent package - 21.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
methylCC 1.26.0
Estimate the cell composition of whole blood in DNA methylation samples
8 versions - Latest release: 5 months ago - 20.8 thousand downloads total - 18 stars on GitHub - 1 maintainer
mitch 1.24.0
Multi-Contrast Gene Set Enrichment Analysis
10 versions - Latest release: 5 months ago - 18.9 thousand downloads total - 18 stars on GitHub - 1 maintainer
Top 7.4% on bioconductor.org
ELMER 2.35.1
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
8 versions - Latest release: 5 months ago - 56.5 thousand downloads total - 1 maintainer
REMP 1.36.0
Repetitive Element Methylation Prediction
4 versions - Latest release: about 2 months ago - 25.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
PoDCall 1.20.0
Positive Droplet Calling for DNA Methylation Droplet Digital PCR
8 versions - Latest release: 5 months ago - 11 thousand downloads total - 1 maintainer
methylscaper 1.20.0
Visualization of Methylation Data
8 versions - Latest release: 4 months ago - 14.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
conumee 1.46.0
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
7 versions - Latest release: 5 months ago - 43.6 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
methylKit 1.38.0
DNA methylation analysis from high-throughput bisulfite sequencing results
8 versions - Latest release: 5 months ago - 3 dependent packages - 175 thousand downloads total - 263 stars on GitHub - 2 maintainers
methylMnM 1.50.0
detect different methylation level (DMR)
7 versions - Latest release: 5 months ago - 1 dependent package - 41.7 thousand downloads total
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
ramwas 1.36.0
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
7 versions - Latest release: 5 months ago - 35.1 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
DSS 2.60.0
Dispersion shrinkage for sequencing data
8 versions - Latest release: 5 months ago - 10 dependent packages - 221 thousand downloads total - 2 maintainers
iNETgrate 1.10.0
Integrates DNA methylation data with gene expression in a single gene network
7 versions - Latest release: 5 months ago - 16.1 thousand downloads total - 65 stars on GitHub - 1 maintainer
EnMCB 1.24.0
Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models
7 versions - Latest release: 5 months ago - 23 thousand downloads total - 9 stars on GitHub - 1 maintainer
BEclear 2.28.0
Correction of batch effects in DNA methylation data
7 versions - Latest release: 4 months ago - 34.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
ramr 1.20.2
Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
8 versions - Latest release: 10 days ago - 20.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
knowYourCG 1.8.2
Functional analysis of DNA methylome datasets
9 versions - Latest release: 10 days ago - 11.4 thousand downloads total - 6 stars on GitHub - 1 maintainer
methylclock 1.18.0
Methylclock - DNA methylation-based clocks
7 versions - Latest release: 4 months ago - 30.5 thousand downloads total - 55 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
MassArray 1.64.0
Analytical Tools for MassArray Data
7 versions - Latest release: 4 months ago - 41.4 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
wateRmelon 2.18.0
Illumina DNA methylation array normalization and metrics
7 versions - Latest release: 5 months ago - 5 dependent packages - 204 thousand downloads total - 1 maintainer
Top 5.6% on bioconductor.org
sesame 1.30.1
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
11 versions - Latest release: 3 months ago - 4 dependent packages - 110 thousand downloads total - 84 stars on GitHub - 1 maintainer
iCheck 1.42.0
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
7 versions - Latest release: 5 months ago - 30.6 thousand downloads total - 1 maintainer
SingleMoleculeFootprinting 2.5.0
Analysis tools for Single Molecule Footprinting (SMF) data
7 versions - Latest release: 5 months ago - 13.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
TCGAbiolinks 2.40.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
9 versions - Latest release: 5 months ago - 7 dependent packages - 652 thousand downloads total - 355 stars on GitHub - 2 maintainers
methyLImp2 1.8.0
Missing value estimation of DNA methylation data
5 versions - Latest release: 5 months ago - 12.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
COCOA 2.26.0
Coordinate Covariation Analysis
7 versions - Latest release: 5 months ago - 27.1 thousand downloads total - 1 maintainer
epialleleR 1.20.0
Fast, Accurate, Epiallele-Aware Methylation Caller and Reporter
7 versions - Latest release: 5 months ago - 19.9 thousand downloads total - 7 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 Data
1 version - Latest release: almost 3 years ago - 4.09 thousand downloads total - 4 stars on GitHub - 1 maintainer
TransView 1.54.0 removed
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
8 versions - Latest release: 7 months ago - 29.7 thousand downloads total - 1 maintainer
bigmelon 1.38.0
Illumina methylation array analysis for large experiments
7 versions - Latest release: 5 months ago - 34.1 thousand downloads total - 1 maintainer
Top 10.0% on bioconductor.org
EpiDISH 2.28.0
Epigenetic Dissection of Intra-Sample-Heterogeneity
7 versions - Latest release: 4 months ago - 2 dependent packages - 77.2 thousand downloads total - 57 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: over 1 year ago - 24.4 thousand downloads total - 1 maintainer
GEM 1.38.0
GEM: fast association study for the interplay of Gene, Environment and Methylation
7 versions - Latest release: 4 months ago - 25.5 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: almost 3 years ago - 16 thousand downloads total - 1 maintainer
les 1.62.0
Identifying Differential Effects in Tiling Microarray Data
7 versions - Latest release: 5 months ago - 1 dependent package - 44.2 thousand downloads total - 1 maintainer
DAMEfinder 1.24.0
Finds DAMEs - Differential Allelicly MEthylated regions
7 versions - Latest release: 5 months ago - 26.8 thousand downloads total - 9 stars on GitHub - 1 maintainer
MethylMix 2.42.0
MethylMix: Identifying methylation driven cancer genes
7 versions - Latest release: 4 months ago - 43.2 thousand downloads total - 1 maintainer
iscream 1.2.0
Make fast and memory efficient BED file queries, summaries and matrices
2 versions - Latest release: 4 months ago - 7.82 thousand downloads total - 0 stars on GitHub - 1 maintainer
hummingbird 1.22.0
Bayesian Hidden Markov Model for the detection of differentially methylated regions
4 versions - Latest release: about 2 months ago - 18 thousand downloads total - 1 maintainer
MIRA 1.34.0
Methylation-Based Inference of Regulatory Activity
7 versions - Latest release: 5 months ago - 1 dependent package - 29.8 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
BiSeq 1.52.0
Processing and analyzing bisulfite sequencing data
8 versions - Latest release: 5 months ago - 59.9 thousand downloads total - 1 maintainer
methylSig 1.24.0
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
7 versions - Latest release: 4 months ago - 23 thousand downloads total - 15 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
DMRcate 3.8.0
Methylation array and sequencing spatial analysis methods
15 versions - Latest release: 4 months ago - 2 dependent packages - 219 thousand downloads total - 1 maintainer
deconvR 1.18.0
Simulation and Deconvolution of Omic Profiles
8 versions - Latest release: 5 months ago - 21.6 thousand downloads total - 9 stars on GitHub - 1 maintainer
scMET 1.14.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity
7 versions - Latest release: 5 months ago - 16.6 thousand downloads total - 18 stars on GitHub - 1 maintainer
Top 8.6% on bioconductor.org
MethylSeekR 1.52.0
Segmentation of Bis-seq data
7 versions - Latest release: 5 months ago - 2 dependent packages - 55.6 thousand downloads total - 1 maintainer
scmeth 1.32.0
Functions to conduct quality control analysis in methylation data
7 versions - Latest release: 5 months ago - 1 dependent package - 25.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
borealis 1.16.0
Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution
7 versions - Latest release: 5 months ago - 15.5 thousand downloads total - 1 maintainer
epimutacions 1.16.2
Robust outlier identification for DNA methylation data
9 versions - Latest release: 23 days ago - 17.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
pathwayPCA 1.28.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
7 versions - Latest release: 4 months ago - 1 dependent package - 24.7 thousand downloads total - 11 stars on GitHub - 1 maintainer
Harman 1.40.0
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
7 versions - Latest release: 5 months ago - 1 dependent package - 41.9 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
missMethyl 1.46.0
Analysing Illumina HumanMethylation BeadChip Data
8 versions - Latest release: 4 months ago - 5 dependent packages - 206 thousand downloads total - 4 maintainers
betaHMM 1.8.0
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Be...
7 versions - Latest release: 5 months ago - 12.8 thousand downloads total - 1 maintainer
mCSEA 1.32.0
Methylated CpGs Set Enrichment Analysis
9 versions - Latest release: 5 months ago - 1 dependent package - 29.3 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
RnBeads 2.30.0
RnBeads
7 versions - Latest release: 5 months ago - 1 dependent package - 94.2 thousand downloads total - 1 maintainer
TurboNorm 1.60.0
A fast scatterplot smoother suitable for microarray normalization
7 versions - Latest release: 4 months ago - 41 thousand downloads total - 1 maintainer
ARRmNormalization 1.52.0
Adaptive Robust Regression normalization for Illumina methylation data
7 versions - Latest release: 5 months ago - 37.4 thousand downloads total - 1 maintainer
Related Keywords
Software 126 Epigenetics 51 DifferentialMethylation 49 Sequencing 44 MethylationArray 42 Microarray 39 Preprocessing 34 GeneExpression 30 ImmunoOncology 30 QualityControl 26 MethylSeq 26 TwoChannel 20 DataImport 18 Normalization 18 DifferentialExpression 17 Coverage 17 Regression 15 Genetics 15 GeneRegulation 14 Visualization 13 CpGIsland 13 Transcription 12 SingleCell 12 RNASeq 11 MultipleComparison 10 StatisticalMethod 10 Transcriptomics 9 BiomedicalInformatics 9 CopyNumberVariation 9 GeneSetEnrichment 8 Clustering 8 WholeGenome 8 Pathways 8 Network 8 dna-methylation 8 BatchEffect 8 ChIPSeq 7 PrincipalComponent 7 Survival 7 FunctionalGenomics 7 SNP 6 Bayesian 6 GenomeWideAssociation 6 GenomeAnnotation 6 SystemsBiology 6 methylation 6 bioconductor 5 FeatureExtraction 5 OneChannel 5 GeneTarget 4 Proteomics 4 GeneticVariability 4 GenomicVariation 4 bioinformatics 4 Classification 4 BiologicalQuestion 4 bioconductor-package 3 HiddenMarkovModel 3 KEGG 3 r 3 CellBiology 3 DataRepresentation 3 MultiChannel 3 ATACSeq 2 Infrastructure 2 NucleosomePositioning 2 r-package 2 epimutation 2 next-generation-sequencing 2 NetworkEnrichment 2 GenePrediction 2 DimensionReduction 2 Spatial 2 TimeCourse 2 LongRead 2 MotifAnnotation 2 mRNAMicroarray 2 GraphAndNetwork 2 dna-methylation-data 2 GUI 2 Annotation 2 omics 2 bayesian-inference 2 inheritance 2 samtools 1 Metabolomics 1 Lipidomics 1 GeneSignaling 1 MassSpectrometry 1 ancestry 1 pathway-analysis 1 gene-seq-analysis 1 gene-regulation 1 Reactome 1 epigenetics 1 genetics 1 inference 1 tcgabiolinks 1 machine-learning 1 tcga-data 1