Biocview "DataRepresentation"

A Bioconductor package for accessing GA4GH API data servers

A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

A `DataFrame` (`S4Vectors`) backend for `dplyr`

A fluent interface for manipulating GenomicRanges

A framework for rapid prototyping with file-based data structures

A framework for sharing interactive data and plots from R through the web

A GatingML Interface for Cross Platform Cytometry Data Sharing

A Model-Database Interface to Make the Database Layer Abstract

An alternative to dendrogram visualization and insertion of multiple layers of information

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 Illumina microarray data [A DRAFT - TRUE]

Analysis of Large Affymetrix Microarray Data Sets

Analysis tools for Single Molecule Footprinting (SMF) data

Analyze comorbidities from electronic health record data

An extension of the bigmemory package with added safety, convenience, and a factor class

An R package facilitating analysis of RNA modifications, structures, and interactions

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 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 Simple Data Management and Sharing Tool

A Thin Wrapper around the ImmuneSpace Data and Tools Portal

A Thin Wrapper around the ImmuneSpace Database

A Tool for Customizable and Reproducible Plotting of Sequencing Coverage Data

A tool for unsupervised projection of single cell RNA-seq data

A t-SNE framework to visualize OMICs data

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 for Storing Genomic Interaction Data

Base package for enabling powerful shiny web displays of Bioconductor objects

Bioconductor Algorithms for Big Data

Bioconductor Management with Portable Encapsulated Project (PEP) Objects

Build Haplotye and Generate Figures

Bumpy Matrix of Non-Scalar Objects

chroGPS2: Generation, visualization and differential analysis of epigenome maps

C++ infrastructure for representing and interacting with the gated cytometry data

Classes and Methods for Handling Genomic Interaction Data

Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

CMap Tools in R

co-expressed gene-set enrichment analysis

Compiling Bioconductor to Handle Each Matrix Type

Comprehensive analysis of transciptome data

Comprehensive analysis of transcriptome data

Container for PhIP-Seq Experiments

Convenience package for solving some liftover challenges

Conveniently access PyRanges functionalities from Bioconductor

Conversion Between scRNA-seq Objects

Convert the GatingSet from Boost serialization to protocol buffer format

Copy-Number Analysis of Large Microarray Data Sets

Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

COVID-19 data resources and analysis tools

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Creating a DelayedMatrix of Regression Residuals

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

Delayed Arrays of Random Values

Delayed?Array with remote, e.g., HDF5Server or BigQuery, back end

Delayed operation on DataFrame using standard DataFrame metaphor

Determination of essential phenotypic elements of clusters in high-dimensional entities

Differential Coverage package

Differential Enrichment analysis of Proteomics data

Discern RNA structure proximal to protein binding

Display heatmap at different resolution level of a tree

Displaying binary trees with focus on dendrogram leaves

doseLM

doseR

Efficient compression and analysis of Hi-C Data

Efficient graph representation and manipulation in Bioconductor

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

Extract and manage matrix data from the Human Cell Atlas project

Fast treatment of MACSQuantify FACS data

Find/fix old serialized S4 instances

flexible pipelines for secretome prediction

flowPlots: analysis plots and data class for gated flow cytometry data

Foundation of array-like containers in Bioconductor

Foundation of external vector representation and manipulation in Bioconductor

Foundation of integer range manipulation 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

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

Generic and Biological Sequences

Genometric Correlation package

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Genomic Visualizations in R

Global visualization tool of genomic data

HDF5 backend for DelayedArray objects

HDF5 datasets as array-like objects in R

HDF5 Delayed Array for Nifti Objects

Hierarchical Gating Pipeline for flow cytometry data

High-performance sparse data representation and manipulation in R

High-Throughput Sequence Analysis using the Aroma Framework

Identifying differential DNA loops from chromatin topology data

ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

immune Cell Analysis Tool

Implementation of MultiDataSet and ResultSet

Implementation of the dot bracket annotations with Biostrings

Infer organism and identifier type given a list of genes

Infrastructure for Biostrings-based genome data packages

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 SpatialExperiment with Simple Features in sf

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

Large-scale single-cell RNA-seq data manipulation with GDS files

LC/MS Metabolomics Data Processing Utilities

LoomExperiment container

Main Existing Human Datasets

Manages subsets of data with Bioconductor Experiment objects

Manipulate Zarr archives as R objects

Manipulating and exploring protein and proteomics data

Marker Enrichment Modeling (MEM)

Microbial Comparative Genomics in R

Minimized Single-Cell Consensus Clustering

Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Multiomic Batch effect Correction

NEUral network-based single-Cell Annotation tool

Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies

OmniPath web service client

OmniPath web service client and more

Ontology traversal and search

OSAT: Optimal Sample Assignment Tool

Out-of-core statistical computing and signal processing

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

Phenotypic EMD for comparison of single-cell samples

PhyloProfile

PhyloProfileCorona

PhyloProfileRibi

pipeComp pipeline benchmarking framework

Provides shiny modules to visualize sparrow results

psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders

Randomize Samples for -omics Profiling

Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

Reconstruction, visualization and analysis of branching trajectories

Repertoire Credibility

Representation and manipulation of genomic intervals

Representation and manipulation of genomic intervals; demo with github actions binary generation

Representation and Manipulation of Genomic Tuples

Representation of Sparse Experiments and Assays Across Samples

Representation of SQL database in DataFrame metaphor

Representation of SQL tables in DataFrame metaphor

Representing GDS files as array-like objects

Representing Indexed Relationships Between Features

Representing on-disk / remote VCF files as array-like objects

R framework for exploration and analysis of respirometry data

RImmPort: Enabling Ready-for-analysis Immunology Research Data

RNA-Seq Utilities

R objects for common work flow language representation

Routines that don't belong to the core flow packages yet.

R package for sparse and out-of-core arithmetic and decomposition of Tensor

R SDK for BaseSpace RESTful API

R utilities for rabix.

S4 Classes for Single Cell Data

S4 Class for Spatial Experiments handling

S4 Class for Spatially Resolved -omics Data

S4 implementation of vector-like and list-like objects

Save Delayed Operations to a HDF5 File

Sequential Flow Cytometry Data Gating

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 Consensus Clustering

Single Cell - R Analysis Toolbox

Single-Cell RNA-Seq Utilities

Software for the integration of multi-omics experiments in Bioconductor

Software infrastructure for efficient representation of full genomes and their SNPs

spatialHeatmap

Spatial Overlay for Omic Data from Nanostring GeoMx Data

Spatial Transcriptomics Analysis

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

Summary Statistics for Rows and Columns of Sparse Matrices

Test Single Package Builder

The Cancer Genome Atlas Data Integration

Tidy Meta Profiles using Bioconductor and the Tidyverse

Tools for building SNPlocs data packages

Tools for counting and visualising mutations in a target location

Tools for making reports in various formats

Tools for matrices with precision weights, test and explore weighted or sparse data

Tools for processing of high-dimensional cytometry data

Tools for the Analysis of Ratiometric Data

Tools for visualizing genomics data

tools for working with AMARETTO outputs

Track Cells, Analyze Cell Trajectories and Compute Migration Statistics

Transcript Annotation Tool (TransAT): an R package for retrieving annotations for transcript specific genetic variants

TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

TSS sequencing data analysis

TVTB: The VCF Tool Box

Using TileDB as a DelayedArray Backend

Utilities for handling genomic interaction data

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Visual and interactive gene expression analysis

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 [option]

Working with modified nucleotide sequences

You Only Lookup One (small part of an otherwise large matrix)

Zwyx

Biocview "DataRepresentation"

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