Biocview "DataRepresentation"

A Bioconductor package for accessing GA4GH API data servers
A Bioconductor package for accessing GA4GH API data servers
A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data
A fluent API for accessing multi-assay high-throughput genomics data
A fluent API for accessing multi-assay high-throughput genomics data
A fluent interface for manipulating GenomicRanges
A fluent interface for manipulating GenomicRanges
A framework for rapid prototyping with file-based data structures
A framework for rapid prototyping with file-based data structures
A framework for sharing interactive data and plots from R through the web
A framework for sharing interactive data and plots from R through the web
A GatingML Interface for Cross Platform Cytometry Data Sharing
A GatingML Interface for Cross Platform Cytometry Data Sharing
An alternative to dendrogram visualization and insertion of multiple layers of information
An alternative to dendrogram visualization and insertion of multiple layers of information
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis of Agilent Microarray Data [draft]
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
Analysis of Illumina microarray data [A DRAFT - TRUE]
Analysis of Large Affymetrix Microarray Data Sets
Analysis of Large Affymetrix Microarray Data Sets
Analyze comorbidities from electronic health record data
An extension of the bigmemory package with added safety, convenience, and a factor class
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
An R package for RNA visualization and analysis
A package for importing and analyzing data from Roche's Genome Sequencer System
A package for visualization and extract details
A package for visualization and extract details
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
A RangedSummarizedExperiment with methods for copy number analysis
A rectangular data container where the rows are variables and the columns observations
A search tool for single cell RNA-seq data by gene lists
A search tool for single cell RNA-seq data by gene lists
A Thin Wrapper around the ImmuneSpace Database
A Thin Wrapper around the ImmuneSpace Database
A tool for unsupervised projection of single cell RNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations.
A t-SNE framework to visualize OMICs data
A unified framework for working transparently with on-disk and in-memory array-like datasets
A unified framework for working transparently with on-disk and in-memory array-like datasets
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes for Storing Genomic Interaction Data
Base Classes for Storing Genomic Interaction Data
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
bcbio RNA-Seq
bcbio RNA-Seq
bcbio Single-Cell RNA-Seq
bcbio Single-Cell RNA-Seq
Bioconductor Algorithms for Big Data
Bioconductor Management with Portable Encapsulated Project (PEP) Objects
chroGPS2: Generation, visualization and differential analysis of epigenome maps
C++ infrastructure for representing and interacting with the gated cytometry
Classes and Methods for Handling Genomic Interaction Data
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
CMap Tools in R
CMap Tools in R
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
Compiling Bioconductor to Handle Each Matrix Type
Compiling Bioconductor to Handle Each Matrix Type
Comprehensive analysis of transciptome data
Comprehensive analysis of transcriptome data
Convenience package for solving some liftover challenges
Convenience package for solving some liftover challenges
Conveniently access PyRanges functionalities from Bioconductor
Convert the GatingSet from Boost serialization to protocol buffer format
Copy-Number Analysis of Large Microarray Data Sets
Copy-Number Analysis of Large Microarray Data Sets
Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
Data management of large-scale whole-genome sequence variant calls
Data management of large-scale whole-genome sequence variant calls
DeepBlueR
DeepBlueR
DeepBlueR
Delayed?Array with remote, e.g., HDF5Server or BigQuery, back end
Delayed?Array with remote, e.g., HDF5Server or BigQuery, back end
Delayed operation on DataFrame using standard DataFrame metaphor
Delayed operation on DataFrame using standard DataFrame metaphor
DESeq2 Analysis Utilities
DESeq2 Analysis Utilities
Determination of essential phenotypic elements of clusters in high-dimensional entities
Determination of essential phenotypic elements of clusters in high-dimensional entities
Differential Coverage package
Differential Enrichment analysis of Proteomics data
Differential Enrichment analysis of Proteomics data
Differential Enrichment analysis of Proteomics data
Display heatmap at different resolution level of a tree
doseLM
doseR
doseR
doseR
doseR
doseR
doseR
Efficient compression and analysis of Hi-C Data
Efficient graph representation and manipulation in Bioconductor
Efficient graph representation and manipulation in Bioconductor
Efficient graph representation and manipulation in Bioconductor
Efficient manipulation of biological strings
Efficient manipulation of biological strings
Efficient manipulation of biological strings
Efficient Manipulation of Sparse Experiment Data
exploratory data analysis of tabula muris droplet counts
Exposome exploration and outcome data analysis
Exposome exploration and outcome data analysis
Extract and manage matrix data from the Human Cell Atlas project
FacileData API wrappers over Bioconductor assay containers
FacileData API wrappers over Bioconductor assay containers
Fast treatment of MACSQuantify FACS data
Fast treatment of MACSQuantify FACS data
flexible pipelines for secretome prediction
flowPlots: analysis plots and data class for gated flow cytometry data
Foundation of external vector representation and manipulation in Bioconductor
Foundation of integer range manipulation in Bioconductor
Foundation of integer range manipulation in Bioconductor
Foundation of vector-like and list-like containers in Bioconductor
Foundation of vector-like and list-like containers in Bioconductor
'fst' backend for DelayedArray objects
Functionality Visualization for Motifs
Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
Further Utilities for Genomic Interactions
Gene Expression Atlas query and gene set enrichment package.
Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions
Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions
Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
Generic and Biological Sequences
Generic and Biological Sequences
Genometric Correlation package
Genomic Visualizations in R
Genomic Visualizations in R
Global visualization tool of genomic data
HDF5 backend for DelayedArray objects
HDF5 backend for DelayedArray objects
HDF5 Delayed Array for Nifti Objects
HDF5 Delayed Array for Nifti Objects
HDF5 Delayed Array for Nifti Objects
HDF5 Delayed Array for Nifti Objects
Hierarchical Gating Pipeline for flow cytometry data
Hierarchical Gating Pipeline for flow cytometry data
High-Throughput Sequence Analysis using the Aroma Framework
Identifying differential DNA loops from chromatin topology data
Identifying differential DNA loops from chromatin topology data
ILoReg enables high-precision cell population identification from scRNA-Seq data
immune Cell Analysis Tool
immune Cell Analysis Tool
Implementation of MultiDataSet and ResultSet
Implementation of MultiDataSet and ResultSet
Implementation of the dot bracket annotations with Biostrings
Implementation of the dot bracket annotations with Biostrings
Import Omnipath network
Import Omnipath network
Infrastructure for Biostrings-based genome data packages
Infrastructure for representing and interacting with gated and ungated cytometry data sets.
Infrastructure for representing and interacting with gated and ungated cytometry data sets.
Integrated Interpretation of Genes
Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive visualization and manipulation of nested networks
IPD IMGT/HLA and IPD KIR database for Homo sapiens
IPD IMGT/HLA and IPD KIR database for Homo sapiens
LoomExperiment container
LoomExperiment container
Manipulate Zarr archives as R objects
Manipulating and exploring protein and proteomics data
Manipulating and exploring protein and proteomics data
Marker Enrichment Modeling (MEM)
Marker Enrichment Modeling (MEM)
Microbial Comparative Genomics in R
Microbial Comparative Genomics in R
Minimized Single-Cell Consensus Clustering
Minimized Single-Cell Consensus Clustering
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Multiomic Batch effect Correction
Ontology traversal and search
OSAT: Optimal Sample Assignment Tool
OSAT: Optimal Sample Assignment Tool
Package for CTDbase data query, visualization and downstream analysis
Package for CTDbase data query, visualization and downstream analysis
Package for enabling powerful shiny web displays of Bioconductor objects
Parses BioPax files and represents them in R
Parses BioPax files and represents them in R
Phenotypic EMD for comparison of single-cell samples
Phenotypic EMD for comparison of single-cell samples
Phenotypic EMD for comparison of single-cell samples
PhyloProfile
PhyloProfile
PhyloProfile
pipeComp pipeline benchmarking framework
Produces Summaries and Plots of Features Distributed Across Genomes
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Representation and manipulation of genomic intervals
Representation and manipulation of genomic intervals
Representation and Manipulation of Genomic Tuples
Representation and Manipulation of Genomic Tuples
Representation of Sparse Experiments and Assays Across Samples
Representation of Sparse Experiments and Assays Across Samples
Representation of SQL database in DataFrame metaphor
Representation of SQL database in DataFrame metaphor
Representing GDS files as array-like objects
Representing GDS files as array-like objects
Representing Indexed Relationships Between Features
Representing on-disk / remote VCF files as array-like objects
Representing on-disk / remote VCF files as array-like objects
Representing on-disk / remote VCF files as array-like objects
R framework for exploration and analysis of respirometry data
R framework for exploration and analysis of respirometry data
RImmPort: Enabling Ready-for-analysis Immunology Research Data
RImmPort: Enabling Ready-for-analysis Immunology Research Data
RImmPort: Enabling Ready-for-analysis Immunology Research Data
RNA-Seq Utilities
RNA-Seq Utilities
R objects for common work flow language representation
Routines that don't belong to the core flow packages yet.
R SDK for BaseSpace RESTful API
R utilities for rabix.
S4 Classes for Single Cell Data
S4 Classes for Single Cell Data
S4 Classes for Single Cell Data
S4 implementation of vector-like and list-like objects
Sequential Flow Cytometry Data Gating
Sequential Flow Cytometry Data Gating
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Single-cell analysis toolkit for gene expression data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single-cell RNA-seq toolkit
Single-cell RNA-seq toolkit
Single-Cell RNA-Seq Utilities
Single-Cell RNA-Seq Utilities
Software for the integration of multi-omics experiments in Bioconductor
Software for the integration of multi-omics experiments in Bioconductor
Software for the integration of multi-omics experiments in Bioconductor
Software for the integration of multi-omics experiments in Bioconductor
Software infrastructure for efficient representation of full genomes and their SNPs
Software infrastructure for efficient representation of full genomes and their SNPs
Spatial Transcriptomics Analysis
Spatial Transcriptomics Analysis
StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub
StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub
Stoichiometry analysis of label-free proteomics data
Summarize, Analyze and Visualize MAF Files
Summarize, Analyze and Visualize MAF Files
Summarize, Analyze and Visualize MAF Files
Summary Statistics for Rows and Columns of Sparse Matrices
Summary Statistics for Rows and Columns of Sparse Matrices
The Cancer Genome Atlas Data Integration
The Cancer Genome Atlas Data Integration
Tidy Meta Profiles using Bioconductor and the Tidyverse
Tools for counting and visualising mutations in a target location
Tools for counting and visualising mutations in a target location
Tools for counting and visualising mutations in a target location
Tools for making reports in various formats
Tools for making reports in various formats
Tools for processing of high-dimensional cytometry data
Tools for processing of high-dimensional cytometry data
Tools for the Analysis of Ratiometric Data
Tools for visualizing genomics data
Tools for visualizing genomics data
tools for working with AMARETTO outputs
TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
Utilities for handling genomic interaction data
Utilities for handling genomic interaction data
Utilities for handling genomic interaction data
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Visual and interactive gene expression analysis
Visual and interactive gene expression analysis
Visual and interactive gene expression analysis
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualizations of expressionSet Bioconductor object
Visualize all edges within a KEGG pathway and overlay LINCS data
Visualize all edges within a KEGG pathway and overlay LINCS data
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
Weighted matrix manipulation, finding components of variation with weighted or sparse data
Weighted matrix manipulation, finding components of variation with weighted or sparse data
Working with modified nucleotide sequences
Working with modified nucleotide sequences
You Only Lookup One (small part of an otherwise large matrix)
You Only Lookup One (small part of an otherwise large matrix)
Zwyx