Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "DifferentialMethylation" keyword
Top 0.6% on bioconductor.org
14 versions - Latest release: 21 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: 21 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
DMRcaller 1.34.0
Differentially Methylated Regions caller3 versions - Latest release: 6 months ago - 17.9 thousand downloads total - 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
shinyepico 1.10.0
ShinyÉPICo3 versions - Latest release: 6 months ago - 3.54 thousand downloads total - 3 stars on GitHub - 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
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
ISLET 1.4.0
Individual-Specific ceLl typE referencing Tool3 versions - Latest release: 6 months ago - 1.63 thousand downloads total - 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: 22 days ago - 1.06 thousand downloads total - 4 stars on GitHub - 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
IWTomics 1.26.0
Interval-Wise Testing for Omics Data3 versions - Latest release: 6 months ago - 9.28 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
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
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
TRESS 1.8.0
Toolbox for mRNA epigenetics sequencing analysis3 versions - Latest release: 6 months ago - 1 dependent package - 3.14 thousand downloads total - 1 maintainer
AMARETTO 1.18.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...3 versions - Latest release: 6 months ago - 7.55 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
SIMD 1.20.0
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site3 versions - Latest release: 6 months ago - 5.7 thousand downloads total - 1 maintainer
msgbsR 1.26.0
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions3 versions - Latest release: 6 months ago - 9.48 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
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
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
SMITE 1.30.0
Significance-based Modules Integrating the Transcriptome and Epigenome3 versions - Latest release: 6 months ago - 11.9 thousand downloads total - 1 stars on GitHub - 2 maintainers
omicRexposome 1.24.3
Exposome and omic data associatin and integration analysis4 versions - Latest release: 3 months ago - 7.99 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
GenomicOZone 1.16.0
Delineate outstanding genomic zones of differential gene activity3 versions - Latest release: 6 months ago - 5.21 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
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
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
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
Top 1.9% on bioconductor.org
3 versions - Latest release: 22 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: 22 days ago - 31 dependent packages - 788 thousand downloads total - 56 stars on GitHub - 1 maintainer
magpie 1.4.0
MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation3 versions - Latest release: 9 days ago - 1.25 thousand downloads total - 0 stars on GitHub - 1 maintainer
MoonlightR 1.30.0
Identify oncogenes and tumor suppressor genes from omics data3 versions - Latest release: 22 days ago - 11.7 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
4 versions - Latest release: 14 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: 14 days ago - 7 dependent packages - 364 thousand downloads total - 274 stars on GitHub - 2 maintainers
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: 14 days ago - 1 dependent package - 54.4 thousand downloads total - 1 maintainer
RnBeads 2.22.0
RnBeads3 versions - Latest release: 14 days ago - 1 dependent package - 54.4 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
4 versions - Latest release: 14 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: 14 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 3.3% on bioconductor.org
3 versions - Latest release: 15 days ago - 5 dependent packages - 122 thousand downloads total - 3 maintainers
missMethyl 1.38.0
Analysing Illumina HumanMethylation BeadChip Data3 versions - Latest release: 15 days ago - 5 dependent packages - 122 thousand downloads total - 3 maintainers
Top 2.4% on bioconductor.org
3 versions - Latest release: 15 days ago - 2 dependent packages - 227 thousand downloads total - 1 maintainer
DiffBind 3.14.0
Differential Binding Analysis of ChIP-Seq Peak Data3 versions - Latest release: 15 days ago - 2 dependent packages - 227 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
nempi 1.12.0
Inferring unobserved perturbations from gene expression data3 versions - Latest release: 21 days ago - 2.89 thousand 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: 23 days ago - 175 downloads total - 1 maintainer
Damsel 1.0.0
Damsel: an end to end analysis of DamID1 version - Latest release: 23 days ago - 0 stars on GitHub - 1 maintainer
dinoR 1.0.0
Differential NOMe-seq analysis1 version - Latest release: 23 days ago - 145 downloads total - 0 stars on GitHub - 1 maintainer
cfTools 1.2.0
Informatics Tools for Cell-Free DNA Study2 versions - Latest release: 6 months ago - 946 downloads total - 5 stars on GitHub - 1 maintainer
exomePeak2 1.14.3
Peak Calling and differential analysis for MeRIP-Seq4 versions - Latest release: 5 months ago - 7.99 thousand downloads total - 23 stars on GitHub - 1 maintainer
Top 10.0% on bioconductor.org
2 versions - Latest release: 6 months ago - 2 dependent packages - 25.5 thousand downloads total - 39 stars on GitHub - 1 maintainer
EpiDISH 2.18.0
Epigenetic Dissection of Intra-Sample-Heterogeneity2 versions - Latest release: 6 months ago - 2 dependent packages - 25.5 thousand downloads total - 39 stars on GitHub - 1 maintainer
DAMEfinder 1.14.0
Finds DAMEs - Differential Allelicly MEthylated regions2 versions - Latest release: 6 months ago - 5.01 thousand downloads total - 9 stars on GitHub - 1 maintainer
SOMNiBUS 1.10.0
Smooth modeling of bisulfite sequencing2 versions - Latest release: 6 months ago - 2.75 thousand downloads total - 1 stars on GitHub - 1 maintainer
methylSig 1.14.0
MethylSig: Differential Methylation Testing for WGBS and RRBS Data2 versions - Latest release: 6 months ago - 5.02 thousand downloads total - 15 stars on GitHub - 1 maintainer
DMCFB 1.16.1
Differentially Methylated Cytosines via a Bayesian Functional Approach3 versions - Latest release: 3 months ago - 4.61 thousand downloads total - 0 stars on GitHub - 1 maintainer
REMP 1.26.0
Repetitive Element Methylation Prediction2 versions - Latest release: 6 months ago - 10.7 thousand downloads total - 2 stars on GitHub - 1 maintainer
DMCHMM 1.24.0
Differentially Methylated CpG using Hidden Markov Model2 versions - Latest release: 6 months ago - 8.33 thousand downloads total - 0 stars on GitHub - 1 maintainer
MAGAR 1.10.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...2 versions - Latest release: 7 months ago - 3.97 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 8.7% on bioconductor.org
2 versions - Latest release: 6 months ago - 1 dependent package - 24 thousand downloads total - 9 stars on GitHub - 1 maintainer
regionReport 1.36.0
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results2 versions - Latest release: 6 months ago - 1 dependent package - 24 thousand downloads total - 9 stars on GitHub - 1 maintainer
methylGSA 1.20.0
Gene Set Analysis Using the Outcome of Differential Methylation2 versions - Latest release: 7 months ago - 11 thousand downloads total - 8 stars on GitHub - 1 maintainer
MethCP 1.13.0 removed
Differential methylation anlsysis for bisulfite sequencing data1 version - Latest release: 8 months ago - 2.97 thousand downloads total - 4 stars on GitHub - 1 maintainer
Related Keywords
Software
65
DNAMethylation
46
Sequencing
33
Epigenetics
29
MethylationArray
22
DifferentialExpression
20
ImmunoOncology
17
GeneExpression
17
Microarray
16
Coverage
15
RNASeq
13
QualityControl
13
MethylSeq
13
Regression
12
Preprocessing
12
DataImport
10
GeneRegulation
10
MultipleComparison
9
Normalization
9
Visualization
8
TwoChannel
8
Network
8
StatisticalMethod
7
Pathways
7
GeneSetEnrichment
7
BatchEffect
6
Genetics
6
Transcription
6
BiomedicalInformatics
6
CopyNumberVariation
5
Bayesian
5
WholeGenome
5
CpGIsland
5
Clustering
5
FunctionalGenomics
5
r
4
ChIPSeq
4
DifferentialPeakCalling
4
PeakDetection
4
Transcriptomics
4
TimeCourse
4
SystemsBiology
4
SingleCell
4
bioconductor
4
GenomeAnnotation
4
HiddenMarkovModel
3
OneChannel
3
MultiChannel
3
Survival
3
NetworkEnrichment
3
ReportWriting
3
ATACSeq
3
CellBiology
3
GenomeWideAssociation
3
FunctionalPrediction
2
PrincipalComponent
2
GenomicVariation
2
methylation
2
mRNAMicroarray
2
SNP
2
dna-methylation
2
GeneticVariability
2
Classification
2
DNASeq
2
BiologicalQuestion
2
AlternativeSplicing
2
DifferentialSplicing
2
Annotation
2
FeatureExtraction
2
inheritance
2
GeneTarget
2
generalized-linear-models
1
logistic-regression
1
HistoneModification
1
DNaseSeq
1
ontology
1
tcgabiolinks
1
tcga-data
1
shiny
1
tcga
1
integrative-analysis
1
gdc
1
bioc
1
Epitranscriptomics
1
derfinder
1
GraphAndNetwork
1
differential-methylation
1
NucleosomePositioning
1
GenePrediction
1
deseq2
1
edger
1
regionreport
1
Spatial
1
PooledScreens
1
rmarkdown
1
NeuralNetwork
1
rnaseq
1
NetworkInference
1
rstats
1
GeneSignaling
1