Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "DNAMethylation" keyword
Top 3.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 92.5 thousand downloads total - 182 stars on GitHub - 2 maintainers
methylKit 1.28.0
DNA methylation analysis from high-throughput bisulfite sequencing results3 versions - Latest release: 6 months ago - 3 dependent packages - 92.5 thousand downloads total - 182 stars on GitHub - 2 maintainers
MIRA 1.24.0
Methylation-Based Inference of Regulatory Activity3 versions - Latest release: 6 months ago - 1 dependent package - 10.5 thousand downloads total - 1 maintainer
Top 5.6% on bioconductor.org
3 versions - Latest release: 12 days ago - 4 dependent packages - 50.3 thousand downloads total - 48 stars on GitHub - 1 maintainer
sesame 1.22.0
SEnsible Step-wise Analysis of DNA MEthylation BeadChips3 versions - Latest release: 12 days ago - 4 dependent packages - 50.3 thousand downloads total - 48 stars on GitHub - 1 maintainer
DMRcaller 1.34.0
Differentially Methylated Regions caller3 versions - Latest release: 6 months ago - 17.9 thousand downloads total - 1 maintainer
deconvR 1.8.0
Simulation and Deconvolution of Omic Profiles3 versions - Latest release: 6 months ago - 3.22 thousand downloads total - 9 stars on GitHub - 1 maintainer
NanoMethViz 2.8.1
Visualise methylation data from Oxford Nanopore sequencing3 versions - Latest release: 6 months ago - 5.55 thousand downloads total - 20 stars on GitHub - 1 maintainer
MPFE 1.38.0
Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data3 versions - Latest release: 6 months ago - 12.5 thousand downloads total - 1 maintainer
TransView 1.46.0
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets3 versions - Latest release: 6 months ago - 21.6 thousand downloads total - 1 maintainer
Top 6.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 7 dependent packages - 296 thousand downloads total - 8 stars on GitHub - 1 maintainer
methylumi 2.48.0
Handle Illumina methylation data3 versions - Latest release: 6 months ago - 7 dependent packages - 296 thousand downloads total - 8 stars on GitHub - 1 maintainer
shinyepico 1.10.0
ShinyÉPICo3 versions - Latest release: 6 months ago - 3.54 thousand downloads total - 3 stars on GitHub - 1 maintainer
MethylAid 1.36.0
Visual and interactive quality control of large Illumina DNA Methylation array data sets3 versions - Latest release: 6 months ago - 18.5 thousand downloads total - 1 maintainer
TOAST 1.16.0
Tools for the analysis of heterogeneous tissues3 versions - Latest release: 6 months ago - 3 dependent packages - 15.7 thousand downloads total - 8 stars on GitHub - 1 maintainer
methylMnM 1.40.0
detect different methylation level (DMR)3 versions - Latest release: 6 months ago - 1 dependent package - 17.6 thousand downloads total
omicsPrint 1.22.0
Cross omic genetic fingerprinting3 versions - Latest release: 6 months ago - 7.42 thousand downloads total - 1 maintainer
Top 7.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 38 thousand downloads total - 1 maintainer
ELMER 2.26.0
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes3 versions - Latest release: 6 months ago - 38 thousand downloads total - 1 maintainer
COHCAP 1.48.0
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data3 versions - Latest release: 6 months ago - 19.8 thousand downloads total - 1 maintainer
HIREewas 1.20.0
Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies3 versions - Latest release: 6 months ago - 5.89 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: 6 months ago - 16 thousand downloads total - 1 maintainer
conumee 1.36.0
Enhanced copy-number variation analysis using Illumina DNA methylation arrays3 versions - Latest release: 6 months ago - 23.8 thousand downloads total - 1 maintainer
SingleMoleculeFootprinting 1.10.0
Analysis tools for Single Molecule Footprinting (SMF) data3 versions - Latest release: 6 months ago - 2.89 thousand downloads total - 2 stars on GitHub - 1 maintainer
dmrseq 1.22.1
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing4 versions - Latest release: 2 months ago - 1 dependent package - 17.9 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: 6 months ago - 4.88 thousand downloads total - 1 maintainer
Moonlight2R 1.2.0
Identify oncogenes and tumor suppressor genes from omics data2 versions - Latest release: 21 days ago - 1.06 thousand downloads total - 4 stars on GitHub - 1 maintainer
bigmelon 1.28.0
Illumina methylation array analysis for large experiments3 versions - Latest release: 6 months ago - 12.3 thousand downloads total - 1 maintainer
methylInheritance 1.26.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...3 versions - Latest release: 6 months ago - 1 dependent package - 9.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 8.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 2 dependent packages - 30.1 thousand downloads total - 1 maintainer
MethylSeekR 1.42.0
Segmentation of Bis-seq data3 versions - Latest release: 6 months ago - 2 dependent packages - 30.1 thousand downloads total - 1 maintainer
skewr 1.34.0
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip3 versions - Latest release: 6 months ago - 11.7 thousand downloads total - 1 maintainer
EpiMix 1.4.0
EpiMix: an integrative tool for the population-level analysis of DNA methylation3 versions - Latest release: 6 months ago - 1 dependent package - 1.63 thousand downloads total - 1 stars on GitHub - 1 maintainer
cbaf 1.24.0
Automated functions for comparing various omic data from cbioportal.org3 versions - Latest release: 6 months ago - 8.7 thousand downloads total - 1 maintainer
hummingbird 1.12.0
Bayesian Hidden Markov Model for the detection of differentially methylated regions3 versions - Latest release: 6 months ago - 3.39 thousand downloads total - 1 maintainer
BPRMeth 1.28.0
Model higher-order methylation profiles3 versions - Latest release: 6 months ago - 1 dependent package - 11.9 thousand downloads total - 1 maintainer
methrix 1.16.0
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing3 versions - Latest release: 6 months ago - 1 dependent package - 6.26 thousand downloads total - 27 stars on GitHub - 1 maintainer
GAprediction 1.28.0
Prediction of gestational age with Illumina HumanMethylation450 data3 versions - Latest release: 6 months ago - 9.4 thousand downloads total - 1 maintainer
Harman 1.30.0
The removal of batch effects from datasets using a PCA and constrained optimisation based technique3 versions - Latest release: 6 months ago - 1 dependent package - 20.4 thousand downloads total - 1 maintainer
methimpute 1.24.0
Imputation-guided re-construction of complete methylomes from WGBS data3 versions - Latest release: 6 months ago - 8.86 thousand downloads total - 1 maintainer
scMET 1.4.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity3 versions - Latest release: 6 months ago - 1.73 thousand downloads total - 18 stars on GitHub - 1 maintainer
qsea 1.28.0
IP-seq data analysis and vizualization3 versions - Latest release: 6 months ago - 11.3 thousand downloads total - 1 maintainer
MethylMix 2.32.0
MethylMix: Identifying methylation driven cancer genes3 versions - Latest release: 6 months ago - 22.2 thousand downloads total - 1 maintainer
planet 1.10.0
Placental DNA methylation analysis tools3 versions - Latest release: 6 months ago - 1 dependent package - 5.94 thousand downloads total - 1 maintainer
recountmethylation 1.12.0
Access and analyze public DNA methylation array data compilations3 versions - Latest release: 6 months ago - 4.05 thousand downloads total - 8 stars on GitHub - 1 maintainer
GEM 1.28.0
GEM: fast association study for the interplay of Gene, Environment and Methylation3 versions - Latest release: 6 months ago - 10 thousand downloads total - 1 maintainer
Melissa 1.18.0
Bayesian clustering and imputationa of single cell methylomes3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
methInheritSim 1.24.0
Simulating Whole-Genome Inherited Bisulphite Sequencing Data3 versions - Latest release: 6 months ago - 1 dependent package - 8.46 thousand downloads total - 1 stars on GitHub - 1 maintainer
normalize450K 1.30.0
Preprocessing of Illumina Infinium 450K data3 versions - Latest release: 6 months ago - 9.45 thousand downloads total - 1 maintainer
MEAL 1.32.0
Perform methylation analysis3 versions - Latest release: 6 months ago - 14.4 thousand downloads total - 1 maintainer
methylPipe 1.36.0
Base resolution DNA methylation data analysis3 versions - Latest release: 6 months ago - 1 dependent package - 21.3 thousand downloads total - 1 maintainer
borealis 1.6.0
Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution3 versions - Latest release: 6 months ago - 1.93 thousand downloads total - 1 maintainer
methylscaper 1.10.0
Visualization of Methylation Data3 versions - Latest release: 6 months ago - 2.84 thousand downloads total - 1 maintainer
MBAmethyl 1.36.0
Model-based analysis of DNA methylation data3 versions - Latest release: 6 months ago - 12.5 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 29.5 thousand downloads total - 1 maintainer
HELP 1.60.0
Tools for HELP data analysis3 versions - Latest release: 6 months ago - 29.5 thousand downloads total - 1 maintainer
mCSEA 1.22.0
Methylated CpGs Set Enrichment Analysis3 versions - Latest release: 6 months ago - 1 dependent package - 9.56 thousand downloads total - 1 maintainer
BiocOncoTK 1.22.2
Bioconductor components for general cancer genomics4 versions - Latest release: about 1 month ago - 9.97 thousand downloads total - 1 maintainer
les 1.52.0
Identifying Differential Effects in Tiling Microarray Data3 versions - Latest release: 6 months ago - 1 dependent package - 25.5 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 26.1 thousand downloads total - 1 maintainer
MassArray 1.54.0
Analytical Tools for MassArray Data3 versions - Latest release: 6 months ago - 26.1 thousand downloads total - 1 maintainer
iCheck 1.32.0
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data3 versions - Latest release: 6 months ago - 12.6 thousand downloads total - 1 maintainer
ENmix 1.38.01
Quality control and analysis tools for Illumina DNA methylation BeadChip3 versions - Latest release: 6 months ago - 27.6 thousand downloads total - 1 maintainer
IntOMICS 1.2.0
Integrative analysis of multi-omics data to infer regulatory networks3 versions - Latest release: 6 months ago - 1.05 thousand downloads total - 0 stars on GitHub - 1 maintainer
funtooNorm 1.26.0
Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit3 versions - Latest release: 6 months ago - 8.74 thousand downloads total - 1 maintainer
MethPed 1.30.0
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes3 versions - Latest release: 6 months ago - 10.3 thousand downloads total - 1 maintainer
GeoTcgaData 2.2.0
Processing Various Types of Data on GEO and TCGA3 versions - Latest release: 6 months ago - 1.61 thousand downloads total - 21 stars on GitHub - 1 maintainer
ramr 1.10.0
Detection of Rare Aberrantly Methylated Regions in Array and NGS Data3 versions - Latest release: 6 months ago - 3.04 thousand downloads total - 0 stars on GitHub - 1 maintainer
PoDCall 1.10.1
Positive Droplet Calling for DNA Methylation Droplet Digital PCR4 versions - Latest release: 4 months ago - 2.84 thousand downloads total - 1 maintainer
BEAT 1.40.0
BEAT - BS-Seq Epimutation Analysis Toolkit3 versions - Latest release: 6 months ago - 17.4 thousand downloads total - 1 maintainer
COCOA 2.16.0
Coordinate Covariation Analysis3 versions - Latest release: 6 months ago - 7.09 thousand downloads total - 1 maintainer
ramwas 1.26.0
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms3 versions - Latest release: 6 months ago - 12 thousand downloads total - 1 maintainer
TurboNorm 1.50.0
A fast scatterplot smoother suitable for microarray normalization3 versions - Latest release: 6 months ago - 23 thousand downloads total - 1 maintainer
ARRmNormalization 1.42.0
Adaptive Robust Regression normalization for Illumina methylation data3 versions - Latest release: 6 months ago - 21.5 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 29.3 thousand downloads total - 1 maintainer
MEDME 1.62.0
Modelling Experimental Data from MeDIP Enrichment3 versions - Latest release: 6 months ago - 29.3 thousand downloads total - 1 maintainer
coMET 1.34.0
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methyl...3 versions - Latest release: 6 months ago - 21.1 thousand downloads total - 1 maintainer
DeepBlueR 1.27.0 removed
DeepBlueR2 versions - Latest release: 6 months ago - 12.8 thousand downloads total - 3 maintainers
Top 9.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 35.7 thousand downloads total - 1 maintainer
BiSeq 1.42.0
Processing and analyzing bisulfite sequencing data3 versions - Latest release: 6 months ago - 35.7 thousand downloads total - 1 maintainer
spiky 1.8.0
Spike-in calibration for cell-free MeDIP3 versions - Latest release: 6 months ago - 2.69 thousand downloads total - 2 stars on GitHub - 1 maintainer
epimutacions 1.6.1
Robust outlier identification for DNA methylation data4 versions - Latest release: 6 months ago - 2.28 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
3 versions - Latest release: 21 days ago - 31 dependent packages - 788 thousand downloads total - 56 stars on GitHub - 1 maintainer
minfi 1.50.0
Analyze Illumina Infinium DNA methylation arrays3 versions - Latest release: 21 days ago - 31 dependent packages - 788 thousand downloads total - 56 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
3 versions - Latest release: 17 days ago - 10 dependent packages - 335 thousand downloads total - 1 maintainer
lumi 2.56.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays3 versions - Latest release: 17 days ago - 10 dependent packages - 335 thousand downloads total - 1 maintainer
MoonlightR 1.30.0
Identify oncogenes and tumor suppressor genes from omics data3 versions - Latest release: 21 days ago - 11.7 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
14 versions - Latest release: 20 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R14 versions - Latest release: 20 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
Top 2.7% on bioconductor.org
4 versions - Latest release: 13 days ago - 7 dependent packages - 364 thousand downloads total - 274 stars on GitHub - 2 maintainers
TCGAbiolinks 2.32.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data4 versions - Latest release: 13 days ago - 7 dependent packages - 364 thousand downloads total - 274 stars on GitHub - 2 maintainers
methylclock 1.10.0
Methylclock - DNA methylation-based clocks3 versions - Latest release: 12 days ago - 6.34 thousand downloads total - 32 stars on GitHub - 1 maintainer
regionalpcs 1.2.0
Summarizing Regional Methylation with Regional Principal Components Analysis2 versions - Latest release: 13 days ago - 801 downloads total - 0 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
3 versions - Latest release: 13 days ago - 1 dependent package - 54.4 thousand downloads total - 1 maintainer
RnBeads 2.22.0
RnBeads3 versions - Latest release: 13 days ago - 1 dependent package - 54.4 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
4 versions - Latest release: 13 days ago - 2 dependent packages - 135 thousand downloads total - 1 maintainer
DMRcate 3.0.0
Methylation array and sequencing spatial analysis methods4 versions - Latest release: 13 days ago - 2 dependent packages - 135 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
4 versions - Latest release: 14 days ago - 10 dependent packages - 146 thousand downloads total - 2 maintainers
DSS 2.52.0
Dispersion shrinkage for sequencing data4 versions - Latest release: 14 days ago - 10 dependent packages - 146 thousand downloads total - 2 maintainers
Top 4.3% on bioconductor.org
3 versions - Latest release: 14 days ago - 1 dependent package - 117 thousand downloads total - 1 maintainer
ChAMP 2.34.0
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC3 versions - Latest release: 14 days ago - 1 dependent package - 117 thousand downloads total - 1 maintainer
iNETgrate 1.2.0
Integrates DNA methylation data with gene expression in a single gene network2 versions - Latest release: 14 days ago - 970 downloads total - 65 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
3 versions - Latest release: 14 days ago - 5 dependent packages - 122 thousand downloads total - 3 maintainers
missMethyl 1.38.0
Analysing Illumina HumanMethylation BeadChip Data3 versions - Latest release: 14 days ago - 5 dependent packages - 122 thousand downloads total - 3 maintainers
Top 3.7% on bioconductor.org
3 versions - Latest release: 14 days ago - 12 dependent packages - 201 thousand downloads total - 34 stars on GitHub - 1 maintainer
bsseq 1.40.0
Analyze, manage and store bisulfite sequencing data3 versions - Latest release: 14 days ago - 12 dependent packages - 201 thousand downloads total - 34 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
3 versions - Latest release: 14 days ago - 5 dependent packages - 132 thousand downloads total - 1 maintainer
wateRmelon 2.10.0
Illumina 450 and EPIC methylation array normalization and metrics3 versions - Latest release: 14 days ago - 5 dependent packages - 132 thousand downloads total - 1 maintainer
Top 5.5% on bioconductor.org
3 versions - Latest release: 14 days ago - 48.6 thousand downloads total - 1 maintainer
MEDIPS 1.56.0
DNA IP-seq data analysis3 versions - Latest release: 14 days ago - 48.6 thousand downloads total - 1 maintainer
mitch 1.16.0
Multi-Contrast Gene Set Enrichment Analysis3 versions - Latest release: 21 days ago - 5.04 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
3 versions - Latest release: 14 days ago - 1 dependent package - 70 thousand downloads total - 52 stars on GitHub - 1 maintainer
RTCGA 1.34.0
The Cancer Genome Atlas Data Integration3 versions - Latest release: 14 days ago - 1 dependent package - 70 thousand downloads total - 52 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
3 versions - Latest release: 14 days ago - 1 dependent package - 70.8 thousand downloads total - 1 maintainer
Repitools 1.50.0
Epigenomic tools3 versions - Latest release: 14 days ago - 1 dependent package - 70.8 thousand downloads total - 1 maintainer
coMethDMR 1.8.0
Accurate identification of co-methylated and differentially methylated regions in epigenome-wide ...3 versions - Latest release: 15 days ago - 2.21 thousand downloads total - 7 stars on GitHub - 1 maintainer
CTexploreR 1.0.0
Explores Cancer Testis Genes1 version - Latest release: 22 days ago - 256 downloads total - 0 stars on GitHub - 1 maintainer
epialleleR 1.12.0
Fast, Epiallele-Aware Methylation Caller and Reporter3 versions - Latest release: 19 days ago - 2.98 thousand downloads total - 3 stars on GitHub - 1 maintainer
biscuiteer 1.18.0
Convenience Functions for Biscuit3 versions - Latest release: 19 days ago - 6.34 thousand downloads total - 5 stars on GitHub - 1 maintainer
knowYourCG 1.0.0
Functional analysis of DNA methylome datasets1 version - Latest release: 22 days ago - 107 downloads total - 2 stars on GitHub - 1 maintainer
betaHMM 1.0.0
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Be...1 version - Latest release: 22 days ago - 175 downloads total - 1 maintainer
methodical 1.0.0
Discovering genomic regions where methylation is strongly associated with transcriptional activity1 version - Latest release: 22 days ago - 158 downloads total - 0 stars on GitHub - 1 maintainer
methyLImp2 1.0.0
Missing value estimation of DNA methylation data1 version - Latest release: 22 days ago - 140 downloads total - 4 stars on GitHub - 1 maintainer
Related Keywords
Software
118
DifferentialMethylation
46
Epigenetics
46
MethylationArray
40
Microarray
39
Sequencing
37
Preprocessing
34
GeneExpression
28
ImmunoOncology
28
QualityControl
26
MethylSeq
25
TwoChannel
20
Normalization
18
Coverage
16
DifferentialExpression
16
DataImport
15
Regression
15
Genetics
14
GeneRegulation
13
CpGIsland
13
Visualization
12
Transcription
10
RNASeq
10
MultipleComparison
9
StatisticalMethod
9
BiomedicalInformatics
8
Clustering
8
BatchEffect
8
Network
8
CopyNumberVariation
8
Transcriptomics
8
SingleCell
8
dna-methylation
7
GeneSetEnrichment
7
PrincipalComponent
7
ChIPSeq
7
Pathways
7
GenomeWideAssociation
6
WholeGenome
6
SNP
6
Bayesian
6
Survival
6
FunctionalGenomics
6
GenomeAnnotation
6
SystemsBiology
6
bioconductor
5
FeatureExtraction
5
methylation
5
OneChannel
5
GeneticVariability
4
BiologicalQuestion
4
Classification
4
r
3
HiddenMarkovModel
3
KEGG
3
bioinformatics
3
MultiChannel
3
DataRepresentation
3
bioconductor-package
3
GeneTarget
3
GenomicVariation
3
ATACSeq
2
mRNAMicroarray
2
GraphAndNetwork
2
next-generation-sequencing
2
GenePrediction
2
Proteomics
2
DimensionReduction
2
CellBiology
2
TimeCourse
2
inheritance
2
GUI
2
NetworkEnrichment
2
NucleosomePositioning
2
Annotation
2
MotifAnnotation
2
missing-values
1
core-services
1
differential-methylation
1
generalized-linear-models
1
enrichment
1
GeneSignaling
1
NetworkInference
1
SupportVectorMachine
1
single-cell-methylation
1
Metabolomics
1
CopyNumber
1
tcgabiolinks
1
tcga-data
1
tcga
1
integrative-analysis
1
gdc
1
bioc
1
Lipidomics
1
rpackage
1
missing-data
1
latent-factor-model
1
batch-effects
1
logistic-regression
1
stochastic-gradient-descent
1