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Topic: DimensionReduction or GraphAndNetwork or Epigenetics

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35 packages on Bioconductor tagged DimensionReduction or GraphAndNetwork or Epigenetics, most distinct IPs first

DimensionReduction, GraphAndNetwork and Epigenetics in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202612,63578
SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsAdi Laurentiu Tarca		Adi Laurentiu Tarcasoftware28 Apr 20261,83915
SC3
Single-Cell Consensus ClusteringVladimir Kiselev		Vladimir Kiselevsoftware28 Apr 20261,36892
STATegRa
Classes and methods for multi-omics data integrationDavid Gomez-Cabrero		David Gomez-Cabrerosoftware28 Apr 20261,18746
scry
Small-Count Analysis Methods for High-Dimensional DataKelly Street		Kelly Streetsoftware28 Apr 20261,14445
snifter
R wrapper for the python openTSNE libraryAlan O'Callaghan		Alan O'Callaghansoftware28 Apr 20261,03325
sevenC
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifsJonas Ibn-Salem		Jonas Ibn-Salemsoftware28 Apr 202690183
scTensor
Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decompositionKoki Tsuyuzaki		Koki Tsuyuzakisoftware28 Apr 2026868231
sincell
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq dataMiguel Julia		Miguel Juliasoftware6 May 202685451
SBMLR
SBML-R Interface and Analysis ToolsTomas Radivoyevitch		Tomas Radivoyevitchsoftware28 Apr 20268347
scTGIF
Cell type annotation for unannotated single-cell RNA-Seq dataKoki Tsuyuzaki		Koki Tsuyuzakisoftware28 Apr 2026829145
srnadiff
Finding differentially expressed unannotated genomic regions from RNA-seq dataZytnicki Matthias		Zytnicki Matthiassoftware28 Apr 2026827160
splineTimeR
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstructionHerbert Braselmann		Herbert Braselmannsoftware28 Apr 202681661
schex
Hexbin plots for single cell omics dataSaskia Freytag		Saskia Freytagsoftware28 Apr 202681074
SBGNview
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"Weijun Luo		Weijun Luosoftware28 Apr 202679285
syntenet
Inference And Analysis Of Synteny NetworksFabrício Almeida-Silva		Fabrício Almeida-Silvasoftware28 Apr 202678076
spqn
Spatial quantile normalizationYi Wang		Yi Wangsoftware28 Apr 202674943
scBFA
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seqRuoxin Li		Ruoxin Lisoftware28 Apr 2026728200
ssPATHS
ssPATHS: Single Sample PATHway ScoreNatalie R. Davidson		Natalie R. Davidsonsoftware28 Apr 2026725129
scMET
Bayesian modelling of cell-to-cell DNA methylation heterogeneityAndreas C. Kapourani		Andreas C. Kapouranisoftware28 Apr 2026687107
SOMNiBUS
Smooth modeling of bisulfite sequencingKathleen Klein		Kathleen Kleinsoftware28 Apr 2026640144
spatialHeatmap
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data ExtensionsJianhai Zhang		Jianhai Zhangsoftware13 May 2026617116
sparsenetgls
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regressionIrene Zeng		Irene Zengsoftware28 Apr 202659029
StabMap
Stabilised mosaic single cell data integration using unshared featuresShila Ghazanfar		Shila Ghazanfarsoftware28 Apr 202653853
SpiecEasi
Sparse Inverse Covariance for Ecological Statistical InferenceZachary Kurtz		Zachary Kurtzsoftware28 Apr 202652573
scECODA
Single-Cell Exploratory Compositional Data AnalysisChristian Halter		Christian Haltersoftware18 Jun 2026491167
SETA
Single Cell Ecological Taxonomic AnalysisKyle Kimler		Kyle Kimlersoftware28 Apr 202647948
slalom
Factorial Latent Variable Modeling of Single-Cell RNA-Seq DataDavis McCarthy		Davis McCarthysoftware28 Apr 202647773
SingleMoleculeFootprinting
Analysis tools for Single Molecule Footprinting (SMF) dataGuido Barzaghi		Guido Barzaghisoftware4 Nov 2025440136
Site2Target
An R package to associate peaks and target genesPeyman Zarrineh		Peyman Zarrinehsoftware28 Apr 202643224