Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "MethylSeq" 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
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
Guitar 2.18.0
Guitar3 versions - Latest release: 6 months ago - 18.4 thousand downloads total - 1 maintainer
Top 2.9% on bioconductor.org
3 versions - Latest release: 19 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 stars on GitHub - 1 maintainer
karyoploteR 1.30.0
Plot customizable linear genomes displaying arbitrary data3 versions - Latest release: 19 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 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
padma 1.12.0
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis3 versions - Latest release: 6 months ago - 3.61 thousand downloads total - 3 stars on GitHub - 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
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
LOLA 1.32.0
Locus overlap analysis for enrichment of genomic ranges3 versions - Latest release: 6 months ago - 5 dependent packages - 25 thousand downloads total - 1 maintainer
RgnTX 1.4.0
Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and am...3 versions - Latest release: 6 months ago - 1.6 thousand downloads total - 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
regioneReloaded 1.4.0
RegioneReloaded: Multiple Association for Genomic Region Sets3 versions - Latest release: 6 months ago - 1.61 thousand downloads total - 5 stars on GitHub - 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
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
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
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
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
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
Top 2.2% on bioconductor.org
3 versions - Latest release: 14 days ago - 13 dependent packages - 217 thousand downloads total - 1 maintainer
regioneR 1.36.0
Association analysis of genomic regions based on permutation tests3 versions - Latest release: 14 days ago - 13 dependent packages - 217 thousand downloads total - 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 3.4% on bioconductor.org
3 versions - Latest release: 14 days ago - 2 dependent packages - 92.3 thousand downloads total - 1 maintainer
QuasR 1.44.0
Quantify and Annotate Short Reads in R3 versions - Latest release: 14 days ago - 2 dependent packages - 92.3 thousand downloads total - 1 maintainer
Top 5.9% on bioconductor.org
3 versions - Latest release: 14 days ago - 3 dependent packages - 204 thousand downloads total - 1 maintainer
systemPipeR 2.10.0
systemPipeR: workflow management and report generation environment3 versions - Latest release: 14 days ago - 3 dependent packages - 204 thousand downloads total - 1 maintainer
Top 2.4% on bioconductor.org
3 versions - Latest release: 14 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: 14 days ago - 2 dependent packages - 227 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
3 versions - Latest release: 15 days ago - 1 dependent package - 70.8 thousand downloads total - 1 maintainer
Repitools 1.50.0
Epigenomic tools3 versions - Latest release: 15 days ago - 1 dependent package - 70.8 thousand downloads total - 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
dinoR 1.0.0
Differential NOMe-seq analysis1 version - Latest release: 22 days ago - 145 downloads total - 0 stars on GitHub - 1 maintainer
ChromSCape 1.12.0
Analysis of single-cell epigenomics datasets with a Shiny App2 versions - Latest release: 7 months ago - 4.01 thousand downloads total - 13 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
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
methylCC 1.16.0
Estimate the cell composition of whole blood in DNA methylation samples2 versions - Latest release: 6 months ago - 6.03 thousand downloads total - 20 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
epihet 1.16.0 removed
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data1 version - Latest release: 7 months ago - 4.09 thousand downloads total - 3 stars on GitHub - 1 maintainer
Related Keywords
Software
39
DNAMethylation
25
Sequencing
24
Epigenetics
18
DifferentialMethylation
13
ChIPSeq
12
ImmunoOncology
11
Coverage
8
RNASeq
8
DataImport
8
MethylationArray
7
Genetics
7
QualityControl
7
GeneExpression
5
Microarray
5
FunctionalGenomics
5
Clustering
4
GeneRegulation
4
MultipleComparison
4
Transcription
4
Visualization
4
bioconductor
4
Preprocessing
4
CopyNumberVariation
4
DNASeq
4
dna-methylation
3
WholeGenome
3
SNP
3
BatchEffect
3
Regression
3
GeneSetEnrichment
3
PrincipalComponent
3
StatisticalMethod
3
DifferentialPeakCalling
3
ReportWriting
3
ATACSeq
3
Alignment
3
SystemsBiology
3
GenomeAnnotation
3
r
2
Normalization
2
PeakDetection
2
inheritance
2
GenomeWideAssociation
2
CpGIsland
2
RiboSeq
2
BiomedicalInformatics
2
next-generation-sequencing
2
DNaseSeq
2
TwoChannel
2
methylation
2
BiologicalQuestion
2
NucleosomePositioning
2
Pathways
2
SplicedAlignment
2
bioinformatics
2
mRNAMicroarray
1
Network
1
GraphAndNetwork
1
GeneticVariability
1
Infrastructure
1
differential-methylation
1
single-cell
1
WorkflowManagement
1
shiny
1
WorkflowStep
1
epigenomics
1
CellBiology
1
SingleCell
1
ShinyApps
1
Classification
1
Annotation
1
HistoneModification
1
samtools
1
epiallele
1
RIPSeq
1
genome-biology
1
statistical-analysis
1
visualization
1
HighThroughputSequencingData
1
OneChannel
1
data-visualization
1
genome
1
genomics-visualization
1
plotting-in-r
1
rstats
1
BioCarta
1
DataRepresentation
1
analysis
1
cpg
1
differentially-methylated-elements
1
monte-carlo-sampling
1
permutation
1
AlternativeSplicing
1
GUI
1
bisulphite-sequencing
1
simulation
1
aberrant-methylation
1
epimutation
1
methylation-microarrays
1