epiwraps - epiwraps: Wrappers for plotting and dealing with epigenomics data
A set of wrappers to facilitate working with epigenomics data. Includes in particular wrappers for producing multitrack single-regions plots, enrichment heatmaps, bigwig generation, normalization, etc. The focus was put on a simple yet flexible interface.
Last updated
epigeneticssequencingnormalizationvisualization
5.72 score 208 scriptsKODAMA - Knowledge Discovery by Accuracy Maximization
Knowledge Discovery by Accuracy Maximization using KNN or SIMPLS followed by latent-space LDA. The portable source package vendors the MIT-licensed CPU implementation from the standalone 'kodama-cpp' library. Optional developer builds can link the same public interface to NVIDIA CUDA or Apple Metal backends. Reusable nearest-neighbor graphs, graph-aware visualization, preprocessing, and adapters for common single-cell containers are provided.
Last updated
softwareclassificationclusteringdimensionreductiongpupreprocessingvisualizationsinglecellspatialcpp
5.20 score 91 scripts 318 downloadsmesa - Methylation Enrichment Sequencing Analysis
A package for the analysis of methylation enrichment sequencing data (e.g. MBD-seq or MEDIP-seq). This allows for the window-based evaluation of methylation levels (using the 'qsea' package), including functions for determining differentially methylated regions. Many functions are provided for tidyverse style modification of the qseaSet objects originally defined in 'qsea'.
Last updated
sequencingdnamethylationcpgislandpreprocessingnormalizationqualitycontrolvisualizationcopynumbervariationdifferentialmethylationcoveragechipseqchiponchip
5.00 scorespatialdataR - Representation of Python's spatialdata in R
R interface to Python/scverse's 'spatialdata' framework for unified spatial omics data handling. Adheres to OME-NGFF standards, providing lazy, on-disk representations for multiscale images and labels (ZarrArray), as well as points and shapes (DuckDB-backed tables). Includes handling of coordinate transformation systems and spatial utilities for cropping, masking, and querying. Integrates tabular annotations as 'SingleCellExperiment's (via 'anndataR'), enabling interoperable spatial omics workflows across R and Python.
Last updated
dataimportdatarepresentationinfrastructureimmunooncologygeneexpressiontranscriptomicssinglecellspatial
4.97 score 13 scriptsBiocDuckDB - Bioconductor DuckDB Integration and High-Level I/O
Integration package providing high-level Parquet I/O functions and optimized methods for single-cell analysis workflows using DuckDB-backed data structures. Includes readParquet and writeParquet functions for seamless serialization of SummarizedExperiment, SingleCellExperiment, MultiAssayExperiment, and MultiAssaySpatialExperiment objects, plus SQL-optimized implementations of scran and scuttle methods for variance modeling, marker detection, QC metrics, and normalization. This package brings together DuckDBDataFrame, DuckDBArray, DuckDBGRanges, and DuckDBSpatial (optional) for complete Bioconductor integration.
Last updated
dataimportdatarepresentationinfrastructurernaseqsequencingsinglecellsoftware
4.87 score 34 scriptsQFeaturesGUI - A suite of shiny apps to use the main functionalities of the QFeatures package
"QFeaturesGUI is a suite of shiny apps that serve as graphical interfaces for the QFeatures package. Currently, the package contains the following shiny apps: 'importQFeatures'."
Last updated
softwareshinyappsguiproteomicssinglecelldataimportpreprocessing
4.80 scoreMultiAssaySpatialExperiment - Multi-Assay Experiment with Spatial Context
Extends MultiAssayExperiment with spatial context elements (images, labels, points, shapes) for integrative analysis of spatially resolved multi-omics data. Supports coercion to and from SpatialExperiment and SpatialFeatureExperiment.
Last updated
infrastructuredatarepresentation
4.77 score 1 dependents 7 scriptsOmicsLake - OmicsLake: Versioned, On-Disk Omics Data Management for Bioconductor
A lightweight framework for versioned, on-disk omics data management using DuckDB, Arrow, and Parquet. It provides read/write-style functions, snapshots, and version-aware dataset lineage for tracked or explicitly annotated workflows. Adapters preserve supported Bioconductor containers, including SummarizedExperiment and MultiAssayExperiment, while retaining queryable tabular components.
Last updated
infrastructuredataimportdatarepresentation
4.69 score 41 scriptsfastPLS - Fast Partial Least Squares for High-Dimensional Data
Fast implementations of partial least squares models for high-dimensional regression and classification. The package provides compiled implementations of PLS-SVD, SIMPLS, OPLS and kernel PLS, together with truncated singular value decomposition backends, discriminant classifiers, cross-validation utilities and optional CUDA or Apple Metal acceleration when the required system libraries are available.
Last updated
softwaredimensionreductionclassificationregressiongeneexpressionmetabolomicssinglecellgpuopenblascpp
4.63 score 45 scripts 164 downloadsSPAROscore - A package to compute gene signature scores from transcriptomics data
SPAROscore is a gene signature scoring method designed to be robust across diverse gene expression datasets. SPAROscore adapts to varying levels of sparsity, allowing signature scores to be efficiently computed across bulk, single-cell, and spatial transcriptomic datasets. The resulting scores quantify the relative expression of a gene signature compared with the background expression of each sample/cell/domain, making the scores straightforward to interpret biologically. Internally, SPAROscore ranks genes within each column and computes the Spearman footrule distance between the observed ranks of the signature genes and a background gene expression rank estimated from the geometric mean expression of the sample, cell, or spatial domain.
Last updated
geneexpressionsinglecellspatialtranscriptomicsgenesetenrichmentpathwayssoftware
4.52 score
CMEnt - Characterization of Methylation using positional ENTanglement
CMEnt implements a correlation-based method for identifying Differentially Methylated Regions (DMRs) from genomic seeds, commonly Differentially Methylated Positions (DMPs). The package expands regions around significant seeds considering both statistical significance and biological relevance of methylation changes. It supports array-based (450K, EPIC, EPICv2) and NGS methylation data through tabix-indexed files, provides DMR interaction analysis via motif similarity, and includes comprehensive visualization tools including circos plots and beta value heatmaps.
Last updated
dnamethylationdifferentialmethylationepigeneticsstatisticalmethodworkflowstepannotationmethylationarraymotifannotation
4.46 score 17 scriptsgDRplots - 'gDRplots'
gDRplots provides static visualization functions and dedicated helpers for the gDR drug response platform. Designed for high-throughput screening (HTS), pharmacogenomics, and chemical genomics research, it enables comprehensive analysis of single-agent, co-dilution, and drug combination cell viability assays. The package supports quality control (plate layouts, control mapping), data normalization inspection, dose-response curves, distribution boxplots, drug synergy heatmaps with overlaid isobolograms, and combination index plots. Additionally, it integrates with PRISM and DepMap datasets to generate volcano plots and correlation scatter plots for molecular feature associations.
Last updated
softwarevisualizationqualitycontrolnormalizationcellbasedassayspharmacogenomicsmicrotitreplateassay
4.44 score 26 scriptsMagellanNTK - A customizable Workflow Manager
MagellanNTK (Magellan Navigation ToolKit) is a collection of Shiny modules which provide the basis for a generic workflow manager for data processing toolswith several steps. It works in combination with any package which implements data processing pipelines compliant with MagellanNTK such as MSPipelines and Prostar2.
Last updated
softwareguishinyappsworkflowstep
4.43 scoresciNOME - Region-Centric Integration for Single-Cell Multi-Omics
Provides an end-to-end pipeline for processing RNA, DNA methylation, and chromatin accessibility data at the single-cell level. It features ultra-fast data aggregation, quality control, dimensionality reduction, and multi-omics integration based on genomic regions. Additionally, it offers extensive publication-ready visualization tools for downstream analysis.
Last updated
softwaresinglecellepigeneticstranscriptomicsdnamethylationdifferentialexpressiondimensionreductionclusteringqualitycontrol
4.38 scorescMAGeCK - Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data
scMAGeCK is a computational model to identify genes associated with multiple expression phenotypes from CRISPR screening coupled with single-cell RNA sequencing data (e.g. CROP-seq, Perturb-seq). It provides two complementary modules: a rank-based test (scMAGeCK-RRA) that links a perturbation to a single marker or gene signature, and a linear-regression test (scMAGeCK-LR) that estimates the effect of each perturbation on the expression of all genes. The package also estimates single-cell perturbation-response scores to capture heterogeneous perturbation effects across individual cells.
Last updated
crisprsinglecellrnaseqsequencingpooledscreenstranscriptomicsgeneexpressionregressioncpp
4.38 score 60 scriptstTEscanR - An advanced R-based package to quantify and visualize translation efficiency from sequencing data
Translation elongation is dependent on codon-anticodon interactions, with suitable nucleotide pairing being essential for efficient translation. To quantify this relationship, we previously developed a computational pipeline (GitHub - wgao688/sc_tRNA_mRNA) that uses mRNA codon usage relative to tRNA anticodon availability as a proxy for theoretical translation efficiency (tTE). Here, we introduce tTEscanR, a powerful and user-friendly R-based package that extends this approach to quantify translation efficiency from both bulk and single-cell sequencing data. tTEscanR is a versatile tool for exploring translation efficiency in diverse cellular processes, disease mechanisms, and therapeutic development. It also features an advanced visualization module to generate high-quality plots, enhancing result interpretation and communication.
Last updated
softwareepitranscriptomicstranscriptomicsgeneexpressiongeneregulationsequencingsinglecell
4.34 score 1 scriptsmethylTFR - Quantification of DNA Methylation Signatures in TFBS
methylTFR is an extensive R package designed specifically for analyzing DNA methylation signatures within transcription factor binding sites (TFBS) across diverse genomic annotations. It enhances methylation analysis by calculating a bias-corrected 'deviation' in methylation levels, leveraging GC bias distribution and frequency data. This package offers a variety of functions that facilitate the motif activity exhibiting diverse methylation patterns across distinct samples or cells.
Last updated
softwarednamethylationsinglecellstatisticalmethodgeneregulationepigeneticstranscriptionsequencingwholegenomedifferentialmethylationmotifannotationmotifdiscovery
4.27 score 37 scriptsHuMMANet - Curated Paired Human Microbiome-Metabolome Study Data
Provides access to curated paired human microbiome-metabolome study bundles available through Bioconductor ExperimentHub. The package organizes matched sample metadata, species abundance profiles, original and harmonized metabolite profiles, and study-specific annotation resources including metabolite identifier mappings, microbial producer annotations, disease associations, pathway annotations, and drug similarity matches. The resource is designed to support consistent and reproducible cross-study microbiome-metabolome analyses.
Last updated
experimentdataexperimenthubhomo_sapiens_datamicrobiomedata
4.22 scoreIntegratedLearner - Integrated Multi-Omics Learning for Survival and Other Outcomes
Provides a unified interface for multi-omics prediction using early and late fusion for continuous, binary, multiclass, and survival outcomes. It supports both MultiAssayExperiment and PCL-style inputs, performs input validation and feature/sample harmonization across layers, and provides model fitting, prediction, plotting, and variable-importance utilities.
Last updated
softwareclassificationsurvivalmicrobiomeopenjdk
4.22 score 11 scripts
bppg - Bipartite peptide-protein graphs
This package contains functionality to create and characterize bipartite graphs that model the relationship between peptides and proteins in bottom-up proteomics. With these graphs, protein ratios (fold change between two sample groups) are calculated from the respective measured peptide ratios. The main aim is to make use of quantitative information contained in shared peptides and making it possible to quantify proteins without shared peptides. Further, the package offers general analysis of peptide and protein relationships using bipartite graphs and visualization for these graphs.
Last updated
proteomicsgraphandnetworkmassspectrometrymultiplecomparisonvisualization
4.18 score 1 scriptspepitope - Extract, QC and Screen Peptide Epitopes
Supports T cell receptor neoantigen co-culture screen analysis from peptide library design to sequencing quality control and differential abundance testing. The package annotates somatic variants and RNA fusions, extracts mutant and reference peptide context, prepares barcoded minigene construct tables, counts sample and construct barcodes from sequencing data, and identifies immunogenic epitopes in dropout screens.
Last updated
dnaseqvariantannotationimmunooncologyzlibcpp
4.18 score 4 scriptssbivar - Test for Spatial Bivariate Association Across Omics Types
Sbivar implements a suite of tests for Spatial BIVARiate association across omics modalities, with possibly disjoint coordinate sets. Implemented tests are generalized additive models (GAMs), modified t-test, bivariate Moran's I and Gaussian processes (GPs). Both single images and replicated experiments can be analysed.
Last updated
transcriptomicsspatialproteomicsmetabolomicsopenblascpp
4.15 score 4 scriptsreglScatterplotR - Interactive WebGL Scatterplots for Biological Data Exploration
Lightweight 'htmlwidgets' interface to the JavaScript 'regl-scatterplot' library, rendering millions of two-dimensional points in the browser via WebGL. Designed for exploratory visualisation of single-cell, spatial transcriptomics and other high-dimensional biological data. Features include synchronised pan/zoom across multiple plots, categorical and continuous colour mapping, lasso selection, range and category filtering, PNG/SVG/PDF export, and Shiny integration. The widget works in the 'RStudio' Viewer, standalone HTML files, Shiny applications and Jupyter notebooks running the 'IRkernel'.
Last updated
softwarevisualizationsinglecellspatialgeneexpressiontranscriptomicsdimensionreductionshinyapps
4.13 score 15 scripts
pepVet - Evaluate Proteolytic Digests for Proteomics Workflows
Simulates proteolytic digestion, scores the resulting peptides for LC-MS/MS suitability, compares candidate enzymes, and reports digest quality at the protein level. Supports 40 cleaver-compatible enzyme rules, workflow presets, peptide mass and pI calculations, sequence-local cleavage-efficiency annotations, and proteome-aware uniqueness scoring. Evaluates multi-FASTA files in batches with per-protein triage and proteome-level summaries. Exports peptide lists for Skyline and generic downstream tools and prints styled console reports.
Last updated
proteomicsmassspectrometryqualitycontrol
4.08 score 12 scriptsfastEmbedR - Fast Native UMAP and openTSNE Embeddings
Native float32 UMAP and openTSNE-style embeddings from data matrices or precomputed nearest-neighbor indices and distances. One-call workflows use package-native CPU HNSW and Apple Metal exact or IVF-Flat search. Optional CUDA support links directly to FAISS GPU and the RAPIDS cuVS C API while retaining nearest-neighbor results on the device. Preprocessing, graph or affinity construction, fixed-reference transform, and layout optimization use native code with explicit CPU, Metal, and CUDA backend reporting. Optional graph utilities support downstream Louvain, Leiden, and Walktrap community detection.
Last updated
softwarepreprocessingdimensionreductionvisualizationclusteringsinglecellflowcytometrygeneexpressiongpucpp
4.04 scorenormScore - Evaluation and Ranking of Normalization Methods for Proteomics Data
Provides tools to evaluate and rank normalization methods for omics datasets using a composite score derived from multiple performance metrics. The package is designed to support systematic benchmarking and comparison of normalization strategies across datasets and experimental settings. It also includes utilities for summarizing results and visualizing normalization performance.
Last updated
softwareproteomicsnormalizationqualitycontrolpreprocessingmultiplecomparison
4.02 score
QuickBLAST - High-Performance Sequence Alignment using BLAST and Apache Arrow
A BLAST Wrapper to call BLAST directly from R (interoperable and without Sys.call()) coupled with Apache Arrow's columnar format with parquet, IPC and csv file support.
Last updated
softwarealignmentsequencematchingsequencingdataimportlibunwindcppopenmp
4.02 score 3 scriptsCyFj11 - Parse FlowJo V11 Workspace Files and Export to FlowJo V10
Provides functions to parse FlowJo v11 workspace files (.flowjo) and extract gating information, populations, and associated FCS files. Includes utilities for exporting data to FlowJo v10 workspace format. The package enables bidirectional data flow between FlowJo and R/Bioconductor, facilitating reproducible analysis workflows.
Last updated
flowcytometrydataimportinfrastructurepreprocessing
3.88 scorecellpaintr - Perturbation Analysis for Cell Painting Data
This package load cell painting data into R and preprocess feature to make them ready for machine learning. We use random forest to predict cell perturbations from CellProfiler features. We summarize the results in a volcano plot.
Last updated
singlecellsoftwareclassificationfeatureextractionpreprocessingvisualization
3.85 score 1 stars 2 scripts
CorNetto - Knowledge-Guided Multi-Omic Correlation Network Analysis
Builds knowledge-guided multi-omic correlation networks from normalized transcriptomic, proteomic, and metabolomic abundance data. Group-specific correlation networks are compared with the Fisher z-difference test, either across all within-omic pairs in one or every assay without generating cross-omic pairs, or across candidate edges supplied by a prior-knowledge network, and the resulting differential network is summarized into node-level rewiring scores that identify features whose interaction patterns change between groups. Rewiring scores can be compared with group-label permutation reference distributions, and networks can be restricted to pathway-focused neighbourhoods, converted to 'igraph' objects, or exported as Cytoscape-ready node and edge tables. The package is built on Bioconductor containers so that multi-omic assays and sample metadata are managed consistently throughout the workflow.
Last updated
graphandnetworkmetabolomicsnetworknetworkinferenceproteomicssystemsbiologytranscriptomics
3.85 scorespbtest3 - Test Single Package Builder
What the package does (one paragraph).
Last updated
softwaredataimportbiologicalquestion
3.78 score 2 scriptsMOTL - Multi-omics matrix factorization with transfer learning
A transfer learning algorithm for multi-omics matrix factorization called 'MOTL' (Multi-Omics Transfer Learning). 'MOTL' is a Bayesian transfer learning method, based on 'MOFA'. 'MOTL' infers latent factor values for a multi-omics target dataset, consisting of a small number of samples, by incorporating latent factor values already inferred with a 'MOFA' factorization of a large, heterogeneous, learning dataset.
Last updated
dimensionreductionfeatureextractionbayesiannormalization
3.74 scoreLIPIDIFy - Comprehensive Lipidomics Data Analysis with Interactive Visualization
Provides a comprehensive toolkit for end-to-end lipidomics data analysis, including missing value imputation, batch effect correction, normalization, differential abundance analysis using limma and edgeR, gene set enrichment analysis, and extensive visualization capabilities. Lipid names are automatically classified by class, subclass, and fatty-acid saturation. Features both an interactive Shiny interface for bench biologists and fully scriptable R functions for bioinformaticians. Supports flexible custom lipid classification schemes and user-defined enrichment sets.
Last updated
softwarelipidomicsmassspectrometrynormalizationpreprocessingdifferentialexpressiongenesetenrichmentvisualizationshinyappsmultiplecomparisonbatcheffectqualitycontroldataimportclassification
3.65 score 4 scriptsGeneSCARAB - Gene Set Circular Analysis for Rhythms Ascertainment in Bioprocesses
GeneSCARAB includes a range of features designed to enable a robust and comprehensive analysis of the circular distributions of biomolecules (genes, proteins, metabolites, ...) associated with bioprocesses in any species. It is specifically designed for circadian omics studies and facilitates data organization, statistical analysis, and the visualization of results. It works with the output of standard rhythm detection software, such as CircaCompare, MetaCycle or RAIN.
Last updated
geneticsmultiplecomparisonproteomicssoftwaresystemsbiologytimecoursetranscriptomicsstatisticalmethod
3.60 score
grayleafspotr - Quantitative Analysis of Gray Leaf Spot Colonies from Plate Images
Quantitative phenotyping of gray leaf spot (Magnaporthe oryzae) fungal colonies grown on petri dishes. The package segments colonies from time-lapse plate photographs using a bundled SmallUNet deep-learning model, extracts morphometric and texture features (area, eccentricity, crack coverage, radial profile), and provides tidy result objects together with template ggplot2 visualisations. Python dependencies are managed automatically through basilisk; no manual environment setup is required.
Last updated
softwarepreprocessingvisualizationclassificationfeatureextraction
3.60 score 1 stars 6 scriptsfaissR - FAISS-Backed Nearest Neighbours, kNN Models, and k-Means
Native nearest-neighbour search, k-nearest neighbour prediction, and k-means helpers for large dimensionality reduction workflows in high-throughput biological data analysis, including single-cell, flow cytometry, imaging, and mass spectrometry applications. Functional native builds require the FAISS C++ library, including CPU-only indexes, and can optionally use FAISS GPU indexes with NVIDIA cuVS integration or direct RAPIDS cuVS/CUDA indexes on NVIDIA machines. CPU-only systems do not need NVIDIA libraries, but NVIDIA CUDA/cuVS libraries are mandatory when a GPU-enabled build is explicitly requested. Unsupported WebAssembly and Bioconductor staging platforms may build diagnostic-only stubs that report the unavailable native functionality. Supervised kNN models use knn(Xtrain, Ytrain) and predict(), or knn(Xtrain, Ytrain, Xtest) for immediate prediction. Class probabilities are returned through predict(type = "prob") for kNN classification models.
Last updated
softwareinfrastructuregpusinglecellflowcytometrymassspectrometryimagingmassspectrometryproteomicsclusteringdimensionreductionclassificationfortrancppopenmp
3.60 scorescCertify - Explainable Confidence Scoring for Single-Cell Annotations
scCertify provides an explainable framework for assessing the confidence of cell-type annotations in single-cell RNA sequencing data. Confidence scores are computed using marker enrichment, neighborhood agreement, entropy-based uncertainty estimation, and ontology-aware label matching to support transparent interpretation of annotation quality.
Last updated
softwaresinglecellrnaseqgeneexpressionsequencing
3.48 scoreSpectraStash - Serialize and restore Spectra objects in interoperable file formats
The serialization mechanism of R allows to save and load R data objects in a binary format, that can however not be read by other programming languages or software. The SpectraStash package implements the serialization methods from the MsStash package for Spectra objects and its MsBackend classes. A variety of different file formats and types, including HDF5 and JSON-based formats defined by the Bioconductor *alabaster* package are supported. The file type can be defined and configured through a second argument `param` of the save/read methods.
Last updated
infrastructuremassspectrometrymetabolomicsdataimportproteomics
3.48 scoregdscloud - Cloud Storage Access for GDS Files
Provides read-only access to GDS (Genomic Data Structure) files stored on cloud storage services including Amazon S3, Google Cloud Storage (GCS), and Azure Blob Storage, as well as any HTTP/HTTPS URL. Extends the 'gdsfmt' package to transparently open GDS files from cloud URLs (http://, https://, s3://, gs://, az://) using efficient block caching and HTTP Range requests via libcurl.
Last updated
infrastructuredataimportcurlopensslcpp
3.48 score
MRManalyzeR - Process and Analyse Targeted LC-MS Lipidomics and Metabolomics Data
Reproducible post-acquisition processing of targeted LC-MS/MS lipidomics and metabolomics results exported from Waters TargetLynx or from Skyline, or supplied as a plain sample-by-analyte matrix. Reads the quantitative result tables, integrates them with sample and feature metadata, and applies configurable signal filtering (SNR, LOD or LOQ), blank filtering, normalisation, internal-standard and volume adjustment of vendor-reported concentrations, missing-value imputation and batch correction. Each step is an exported function acting on a struct DatasetExperiment; a complete workflow can additionally be driven from a single YAML configuration via run_MRManalyzeR(), which also renders self-contained HTML data-quality and statistical reports. Chromatographic peak detection, peak integration and calibration-curve fitting from raw mass-spectrometry data are outside its scope.
Last updated
metabolomicslipidomicsmassspectrometryqualitycontrolnormalizationbatcheffectvisualizationworkflowstep
3.40 score 5 scriptspolyICSFlow - Identifying the Frequency of Polyfunctional Antigen-Specific T cells in ICS Flow Cytometry Data
polyICSFlow systematically identifies all cytokine combinations detected in an intracellular cytokine staining (ICS) flow cytometry assay and quantifies polyfunctional antigen-specific responses to single or multiple antigens. The package also offers versatile plotting options for efficient data exploration and visualization of cytokine co-expression profiles.
Last updated
flowcytometryimmunologysoftwaresinglecell
3.40 score
ClinicalVariantR - Clinical Variant Interpretation Using ACMG/AMP Germline Criteria
ClinicalVariantR is an interactive Shiny platform for evidence-based germline variant classification under ACMG/AMP 2015 guidelines. It accepts VEP-, SnpEff-, or ANNOVAR-annotated VCF files and applies automated plus curator-guided ACMG criteria. The package supports streaming analysis of large call sets and exports structured per-criterion evidence with reproducibility metadata for clinical review.
Last updated
softwarevariantannotationgeneticssequencingvisualizationguiclassification
3.40 score
ggwas - Modern 'ggplot2' Visualizations for Genome-Wide Association Studies
Create publication-ready visualizations for genome-wide association studies. Provides 20 plot types including Manhattan, QQ, Miami, locus zoom, PheWAS, colocalization, fine-mapping, genetic correlation, SNP density, and density-signal comparison plots. Reads PLINK, REGENIE, GCTA, and GEMMA formats natively. All plot functions return 'ggplot2' objects for full customization. Smart downsampling handles datasets with 10 million+ variants.
Last updated
visualizationgenomewideassociationannotationdataimportsoftware
3.40 score 7 scripts
bHIVE - B-cell Hybrid Immune Variant Engine
The bHIVE package implements an Artificial Immune Network (AI-Net) algorithm for clustering and classification tasks. Inspired by biological immune systems, it employs clonal selection, mutation, and network suppression to analyze and model datasets. This package provides flexible functionality, including affinity metrics, mutation strategies, and hyperparameter tuning.
Last updated
softwareclusteringclassificationnetworkopenblascpp
3.40 score 8 scriptsECLIPSE - ECLIPSE: Enhanced CLonotypic Inference via Prediction of Single-cell Expression
This package is used for the analysis of single-cell T cell receptor sequencing data (scTCR-seq). ECLIPSE maps chain pairings across a sample to predict the true clonotype of each cell, unlike other methods which only consider the chains that are sequenced in each cell. Seurat objects and Cell Ranger vdj/multi contig files are required as inputs.
Last updated
softwaregeneexpressionbiomedicalinformaticsimmunooncologytranscriptomicsclassificationsinglecellannotationsequencing
3.30 score 5 scriptscellchatr - Fast CellChat Database Querying Backed by Rust
Accelerates three bottleneck steps in the CellChat workflow using Rust via extendr. Provides parallel Wilcoxon rank-sum testing with tie correction, HashSet-based gene filtering, and ligand-receptor pair matching as drop-in replacements for CellChat functions. Achieves up to 183x speedup on Wilcoxon testing using Rayon parallelism.
Last updated
singlecellgeneexpressiontranscriptomicsstatisticalmethodsoftwarerustcargo
3.30 scoreSwitchClass - Label-Switch Classification for Baseline- and Perturbation-Aligned Features
Quantifies baseline-aligned and perturbation-aligned molecular features across biological perturbations using a label-switch classification framework. Provides a unified workflow for identifying changes in molecular-feature alignment in longitudinal or comparative omics datasets. Includes tools for classification, visualization, dimension reduction, and pathway enrichment.
Last updated
softwareclassificationfeatureextractiongeneexpressionproteomicstranscriptomicssinglecellpathways
3.30 scoreCySA - Interactive Cluster Selector for Cytometry Data
CySA provides an interactive Shiny-based tool for analyzing flow and mass cytometry data. It supports self-organizing map (SOM) based clustering, dimension reduction (t-SNE, UMAP, PCA), and statistical comparison of cell populations across sample groups. Users can select cell clusters interactively via 2D scatter plots, dendrograms, or SOM node grids, and explore marker expression patterns across the selected populations.
Last updated
singlecellflowcytometryclusteringvisualizationshinyapps
3.30 scoreProtein2Tissue - An R package for tissue expression analysis and gene set enrichment
Protein2Tissue provides a comprehensive framework for analysing tissue-specific gene and protein expression patterns. The package allows users to map genes or proteins to their predominant tissue types, perform tissue-based enrichment analysis on gene sets, and explore expression profiles across a wide range of human tissues. Reference expression data is derived from publicly available databases the Human Protein Atlas (https://www.proteinatlas.org).
Last updated
proteomicstranscriptomicsgenesetenrichmentnetwork
3.30 score 4 scriptsMiCARA - Microbiome Confounder-Adjusted Robust Analysis
Provides a comprehensive framework for multi-cohort microbiome differential abundance and residual correlation analysis. It integrates confounder-adjusted linear models with centered log-ratio transformed taxonomic and functional pathway profiles. The package features robust preprocessing, automated covariate handling, multiple-testing correction, and quality control diagnostics for multi-omics data. Interactive visualization tools are included to facilitate downstream interpretation of cross-domain interaction networks.
Last updated
microbiomedifferentialexpressionsoftwaremetagenomicsnetworkinferencepathwaysnetworkpreprocessingqualitycontrol
3.18 scoreGSE142512 - 450K and EPIC Methylation ExperimentHub Data from GEO
Provides ExperimentHub access to processed DNA methylation resources derived from GEO accession GSE142512. The resources contain Illumina HumanMethylation450 and Infinium MethylationEPIC data represented as RangedSummarizedExperiment objects with beta, M, and CN assays, hg19 genomic ranges, and sample phenotype metadata.
Last updated
experimentdataexperimenthubgeohomo_sapiens_datamethylationarraydatamicroarraydatatissue
3.18 score 4 scriptsPlantTxDbHub - Transcript Database Hub for Plant Genomes
Provides TxDb (transcript database) annotations for plant species. The SQLite files are hosted on Zenodo (or other permanent URLs) and are downloaded on demand via the `downloadPlantTxDbs()` function. The list of available species and their download URLs is maintained in a curated CSV file (inst/extdata/metadata.csv), allowing users and contributors to easily add new databases without modifying R code.
Last updated
annotationdatatxdbarabidopsis_thalianaoryza_sativaglycine_maxsequenceannotation
3.18 scorewoven - Weighted Omics View Embedding via Nystrom for Incomplete Multi-Omics Data
Supervised multi-omics integration for block-missing ("ragged") data. WOVEN learns a shared latent space across V omics modalities using only fully-observed anchor subjects, then projects block-missing subjects via Nystrom extension without feature-level imputation. Supervision via label-augmented cross-covariance (analogous to DIABLO) with optional sparse projection matrices (PMD). Designed for comparative effectiveness research where intersection-only methods introduce selection bias.
Last updated
softwarestatisticalmethodmultiplecomparisongeneexpressiontranscriptomicsproteomicsmetabolomicsdimensionreductionclusteringclassificationsequencing
3.18 score 3 scriptsdmsa - Directional Methylation Set Analysis
Aligns probe-level methylation effects to their predicted effect on gene expression and, for system-level analysis, to each gene's curated polarity with respect to the system's activation tone (e.g. NR3C1 opposes HPA-axis activation). Pools the aligned coefficients with fixed-sign or expected-sign estimators and reports coverage and activation/brake balance per set. Ships the Project Alpha gene-system map, a gene-to-system polarity table carrying a stated source and review flag on every row, and a curated system > module > gene > probe selection cascade whose module labels carry literature-audited evidence tiers and citations; genes without a polarity entry must be specified by the user.
Last updated
dnamethylationdifferentialmethylationmethylationarraygenesetenrichmentgeneexpressionepigeneticsmicroarraycoveragestatisticalmethodmultiplecomparisonregressionsoftware
3.00 score
RhyME - Beta Regression Cosinor Models for Circadian Methylation Analysis
Fits cosinor-based beta regression models for detecting circadian rhythmicity in DNA methylation array data using Template Model Builder (TMB) for efficient likelihood optimization. Supports fixed-effects (cross-sectional) and mixed-effects (repeated measures) designs with configurable period and adjustment covariates. Implements empirical Bayes shrinkage of the beta distribution precision parameter across CpG sites, analogous to limma's moderated variance, to improve genome-wide inference. Provides amplitude, phase, and MESOR estimation on both logit-link and response scales.
Last updated
epigeneticsdnamethylationtimecourseregressiondifferentialmethylationsoftwarecppopenmp
3.00 scoreBatchVaria - Variance-Aware Evaluation of Batch Correction
Evaluates batch correction in omics data by quantifying how a correction redistributes variance, not only whether it removes it. Records correction and variance-decomposition provenance in the metadata of an ordinary SummarizedExperiment, and harmonises both the batch correction methods and the variance-profiling engines behind documented contracts, so that either set can be extended without modifying the package. Variance fractions are compositional, so removing variance associated with one term inflates the fraction attributed to every other. Each decomposition is therefore recorded alongside the total variance it is relative to and the share an unbalanced design cannot attribute to any single term, which is what distinguishes a correction that removed unwanted variation from one that merely removed variation.
Last updated
geneexpressionrnaseqbatcheffectstatisticalmethodsoftwarenormalizationqualitycontroltranscriptomicsdatarepresentationvisualizationsequencing
3.00 scoreTxDb.Athaliana.Ensembl.TAIR10 - Transcripts Annotation Database for Arabidopsis thaliana
TxDb.Athaliana.Ensembl.TAIR10 provides transcript, exon, CDS, and gene annotations for Arabidopsis thaliana based on the TAIR10 reference genome and Ensembl Plants release 63. The TxDb object is built from the Ensembl Plants GFF3 annotation and can be queried using GenomicFeatures accessors such as genes(), transcripts(), exonsBy(), and cdsBy().
Last updated
annotationdatatxdbarabidopsis_thalianasequenceannotationannotationhub
3.00 score
SpaMTP - Spatial Metabolomics and Multi-Omics Analysis
Provides analysis, annotation, visualisation, and multi-omic integration methods for spatial metabolomics data. SpaMTP interoperates with Cardinal, Seurat, and Bioconductor data structures; supports indexed accurate-mass annotation using versioned RaMP resources; and implements spatial feature analysis, pathway enrichment, pathway-network visualisation, and alignment with spatial transcriptomics data.
Last updated
massspectrometryimagingmassspectrometrymetabolomicsspatial
3.00 score 20 scriptsTxDb.Osativa.MSU.RGAP7 - Transcripts Annotation Database for Rice
Provides transcript, exon, and CDS annotations for Oryza sativa (rice) as a Bioconductor TxDb object, generated from the Rice Genome Annotation Project (RGAP) Release 7 / MSU7 GFF3 file (genome assembly IRGSP-1.0). The TxDb object is distributed through AnnotationHub and is retrieved with AnnotationHub(); once loaded it can be queried with standard GenomicFeatures accessors such as genes(), transcripts(), exonsBy(), and cdsBy() to obtain gene models keyed by MSU locus identifiers. The package also provides msu_to_rap() for translating MSU locus identifiers into RAP-DB identifiers.
Last updated
annotationdatatxdboryza_sativasequenceannotationannotationhub
3.00 scoreTxDb.Gmax.JGI.Gmv4 - Transcripts Annotation Database for Soybean
TxDb.Gmax.JGI.Gmv4 provides transcript, exon, and CDS annotations for soybean (Glycine max Wm82.a4.v1). It is a Bioconductor TxDb object built from the official JGI/Phytozome GFF3 annotation and is available via AnnotationHub (retrievable with AnnotationHub()); after loading you can use GenomicFeatures accessors (genes(), transcripts(), exonsBy(), cdsBy()) to extract gene models identified by JGI/Phytozome locus IDs.
Last updated
annotationdatatxdbglycine_maxsequenceannotationannotationhub
3.00 scoreperturbMatch - Match Transcriptomics Signatures to Single-Gene Perturbation References
Matches a query transcriptomics signature against a reference database of single-gene perturbation signatures, ranking the perturbations whose expression response most resembles the query and so nominating the regulators most likely to drive the observed change. Query signatures derived from a differential expression result are scored using cosine, GSEA and signed-Jaccard similarity metrics. Reference databases are supplied as HDF5-backed SummarizedExperiment objects for memory-efficient handling of large perturbation collections, and helper functions rank and visualise the best-matching regulators.
Last updated
generegulationtranscriptomicstranscriptiongenesetenrichmentgenetargetgeneexpressiondifferentialexpression
3.00 score 4 scriptsmdclust - Maximum Diversity Clustering
Standalone implementation of the maximum diversity clustering algorithm (Algorithm 2) from Korsunsky et al. (2019), Nature Methods. Soft spherical k-means with a batch-diversity penalty.
Last updated
softwareclusteringdimensionreductionquartoopenblascpp
3.00 score 5 scriptsmultipletR - Adaptive Detection of Human-Mouse Multiplets in PDX Single-Cell Data
Detects human-mouse multiplets in patient-derived xenograft (PDX) single-cell RNA-seq data using an adaptive threshold method that does not assume a fixed species proportion. Takes a 10x CellRanger GEM classification file and returns the data with added multiplet classifications, with optional diagnostic plots and helpers to annotate a Seurat or SingleCellExperiment object with multiplet classifications or remove multiplets from it.
Last updated
singlecellrnaseqpreprocessingqualitycontroltranscriptomics
3.00 scorervarsim - Variant Simulator with HGVS Notation
Simulates all possible single nucleotide variants (SNVs) across MANE Select transcripts including coding sequence (CDS), untranslated regions (UTRs), and canonical splice sites. Outputs variants in HGVS notation. Provides a comprehensive HGVS toolkit: parsing, syntactic and semantic validation, normalization (3' shifting, common affix trimming), format conversion (HGVS <-> VCF <-> SPDI), transcription mapping (genomic <-> coding), translation to protein consequence, backtranslation from protein to coding variants, variant extraction from sequence alignment, and liftover between genome assemblies.
Last updated
geneticsvariantannotationsnpsequencingtranscriptionvariantdetectionalignmentnormalizationsequencematching
3.00 scoreloopcityData - Experimental Data for the loopcity Package
Provides Hi-C loop calls and chromatin interaction data used in examples and vignettes for the loopcity package. Includes GM12878 Hi-C loop calls at 10 kb resolution (Rao et al. 2014, GSE63525), shipped directly as GInteractions objects. K562 Hi-C contact matrices and CTCF and H3K27ac ChIP-seq signal tracks from Bond et al. 2023 (GSE214123, GSE213908) are hosted on ExperimentHub and retrieved on demand.
Last updated
experimenthubexperimentdatahomo_sapiens_datasequencingdata
3.00 score 7 scriptsTxParq.Hs.gencode.v49 - Parquet-based representation of GENCODE gene models v49 for Homo sapiens
This is a parquet-based representation of GENCODE gene models v49 for Homo sapiens. Parquet is chosen to reduce footprint, to support tidyverse-oriented operations natively, and to provide opportunities for cloud-backed annotation services. Community contributions to functionality and architecture are welcome.
Last updated
infrastructure
3.00 score 5 scriptsmethylTFRAnnotationHg38 - methylTFR Annotations for hg38
Precomputed transcription factor binding sites, motif GC frequency tables and a genome-wide GC distribution for use with the methylTFR package. Binding sites are genome-wide motif matches extended to the footprint window methylTFR reads across; the GC tables record how each motif's sites distribute over genome-wide GC quintiles, which is what allows a deviation score to be corrected for sequence composition. The data are hosted on AnnotationHub and retrieved on first use; this package provides the accessors and the documentation.
Last updated
annotationdataannotationhubfunctionalannotationsequenceannotationhomo_sapiens
2.81 score 13 scriptsDgeaHeatmap - Implementation of Functions to Analyze Nanostring and Other Data for DGE and to Generate Heatmaps
Package for data extraction from Nanostring GeoMx DSP data, also works for other data. Simple functions for Differential Expression Analysis. User-friendly and highly customizable functions for heatmap generation.
Last updated
bayesianclusteringdifferentialexpressiongeneexpressionnormalizationprincipalcomponentrnaseqregressionsequencingsoftwaretranscriptionalternativesplicingbatcheffectbiomedicalinformaticscellbiologycheminformaticsdataimportdifferentialsplicingepigeneticsexonarrayfunctionalgenomicsgenesetenrichmentgeneticsimmunooncologymetabolomicsmicrornaarraymicroarraymultiplecomparisononechannelpreprocessingproprietaryplatformsproteomicsqualitycontrolsystemsbiologytimecoursetwochannelmrnamicroarray
2.81 score 1 starsmethylTFRAnnotationMm10 - methylTFR Annotations for mm10
Precomputed transcription factor binding sites, motif GC frequency tables and a genome-wide GC distribution for use with the methylTFR package. Binding sites are genome-wide motif matches extended to the footprint window methylTFR reads across; the GC tables record how each motif's sites distribute over genome-wide GC quintiles, which is what allows a deviation score to be corrected for sequence composition. The data are hosted on AnnotationHub and retrieved on first use; this package provides the accessors and the documentation.
Last updated
annotationdataannotationhubfunctionalannotationsequenceannotationhomo_sapiens
2.70 score 3 scriptscircaTime - Unified Inference of Circadian Phase from Bulk and Pseudobulk Transcriptomes
Provides a single SummarizedExperiment-based interface to published circadian phase (time-of-sample-collection) inference methods for bulk and donor-level pseudobulk transcriptomes, along with a shared cross-validation benchmarking harness, cross-dataset transfer testing, and a calibrated uncertainty layer: bootstrap and Bayesian confidence intervals validated for real coverage, a fixed or dynamically-selected clock-gene quality flag, and consensus phase estimation across every bundled engine. Does not implement a new phase-inference algorithm; unifies existing published methods that are otherwise scattered across incompatible standalone implementations.
Last updated
softwaregeneexpressiontranscriptomicssequencingmicroarraytimecoursepreprocessing
2.70 score 5 scriptsSpaMTPData - Experiment Data Resources for SpaMTP Workflows
Provides lightweight, version-aware access to spatial metabolomics and multi-omics experiment data used in SpaMTP workflows. Resources cover mouse brain, mouse urinary bladder, simulated single-cell multi-omics, annotation-refinement, and human brain examples. Large files are retrieved and cached through ExperimentHub rather than stored in the package repository.
Last updated
experimentdataexperimenthubhomo_sapiens_datamus_musculus_datareproducibleresearch
2.70 scorehmagmaR - Incorporation of chromatin interaction and epigenetic profiles to predict risk genes
Combines chromatin interaction (e.g. PLAC-seq/Hi-C) data with regulatory region annotations (e.g. promoters, enhancers, H3K27ac) to link non-coding GWAS SNPs to their putative target genes, producing MAGMA-compatible gene annotation files for downstream gene-level association testing.
Last updated
softwareepigeneticschipseqgeneregulationsnpgenomeannotationfunctionalgenomicsgenetargethic
2.70 scoreGENCODEHub - GENCODE AnnotationHub
Provides access through AnnotationHub to genomic annotation resources derived from GENCODE releases. The release 50 collection represents every feature type in the human GRCh38.p14 GTF. Feature-specific GRanges objects retain the imported identifiers and attributes, while a TxDb resource supports gene, transcript, exon, and coding-sequence queries.
Last updated
annotationdataannotationhubgenomicsequencehomo_sapienspackagetypesequenceannotationtxdb
2.70 score 4 scriptsperturbMatchData - Reference Perturbation Signatures from GEO RNA-seq Experiments
Provides the reference perturbation expression signatures used by the perturbMatch package, which ranks the single-gene perturbations whose expression response most resembles a query signature. Each reference signature summarises the differential expression observed after a single-gene perturbation (knockdown, knockout or overexpression) in a human RNA-seq experiment deposited in the Gene Expression Omnibus. Signatures are summarised either by the characteristic direction method or by limma, each with and without surrogate variable analysis batch correction, giving four datasets served as HDF5-backed SummarizedExperiment objects.
Last updated
experimenthubexperimentdataexpressiondatarnaseqdatasequencingdatahomo_sapiens_datageo
2.70 scoredrugannotR - Coordinate-Level Pharmacological Annotation of Genomic Regions
Maps genomic regions to gene features and then to traceable drug-gene relationships. The package preserves genomic coordinates, relationship categories, evidence scope, and source provenance. It deliberately reports coordinate-level pharmacological relevance rather than predicting treatment response, efficacy, toxicity, or dose.
Last updated
annotationdatarepresentationdataimportgenetargetgenomeannotationpharmacogeneticspharmacogenomicsvariantannotation
2.70 score
selexprepR - Preprocessing Public HT-SELEX Sequencing Data
Provides reproducible preprocessing for high-throughput SELEX sequencing data. Supports primer inference, extraction of random regions, sparse sequence counting across rounds, quality control, and provenance manifests. Public-study discovery and checksum-aware ENA FASTQ download planning are included for reproducible data acquisition.
Last updated
softwaredataimportpreprocessingqualitycontrolsequencing
2.70 score 3 scriptsPTMsToPathwaysData - ExperimentHub Data for PTMsToPathways
Companion data package for PTMsToPathways that registers large post-translational modification data resources and intermediate processed data for vignettes in ExperimentHub.
Last updated
experimenthubcancerdatamassspectrometrydata
2.70 scorescOverlay - Multilayer plots for single-cell data
scOverlay provides publication-grade plotting helpers to display a foreground feature (gene expression or metadata) on top of a contextual background (clusters, cell types, samples, or a solid colour) in the same reduced dimension panel, each with independent colour scales (via ggnewscale). It integrates with SingleCellExperiment / SummarizedExperiment, supports flexible subsetting of foreground cells, multiple assays (e.g. counts, logcounts), and grid arrangements by user-defined grouping columns.
Last updated
softwarevisualizationsinglecelltranscriptomicsgeneexpressiondatarepresentation
2.70 score 3 scriptsPACMOSData - ExperimentHub Data for PACMOS
Large reference datasets used by the PACMOS package for multi-omics and MOFA analysis of lung neuroendocrine neoplasms and MESOMICS data.
Last updated
experimentdatahomo_sapiens_datacancerdatasequencingdataexperimenthub
2.70 scoreinferRecom - Homologous Recombination Detection in Family Pedigrees
This package implements a pedigree-based algorithm to detect homologous recombination. Additional functions are supplied to detect runs of homozygosity and to phase haplotypes at informative SNPs.
Last updated
geneticssnpgenomeannotationsequencingcoverage
2.70 scorespbtest5 - Test Single Package Builder
What the package does? (one paragraph).
Last updated
softwaredataimportbiologicalquestion
2.70 scorespatialDESeq - Spatial Differential Expression via Spatial Autoregressive GLMs
Extends negative binomial generalized linear models to spatial transcriptomics by incorporating physical coordinate distance matrices as local smoothing covariates.
Last updated
geneexpressionrnaseqsequencingspatialtranscriptomicsdifferentialexpressionsoftwarecpp
2.00 scoreGO.ddb - Tidy Interface to GO Semantic SQL via DuckDB
Provides a tidyverse-oriented user interface to Gene Ontology data via the Semantic SQL representation, accessed through DuckDB. Replaces the GO.db + AnnotationDbi::select nexus with lazy tibble-based operations for term lookup, ancestor/descendant traversal, and gene-GO annotation queries. The Semantic SQL resource is managed by the ontoProc2 package via BiocFileCache.
Last updated
annotationgoontology
2.00 score 2 scripts