Biocview "Infrastructure"

Accelerated similarity searching of small molecules

Access Bioconductor docker images

Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface

Acid Genomics Base Functions

Acid Genomics Command Line Interface

Acid Genomics Documentation

Acid Genomics Generics

Acid Genomics Genome Annotations

Acid Genomics Single Cell Experiment

Acid Genomics Summarized Experiment

A client for retrieving Bioconductor objects from AnnotationHub

A collection of pre-processing functions

A collection of tools for imaging MS data processing

A compilation of ENCODE metadata

A compilation of metadata from NCBI GEO

A compilation of metadata from NCBI SRA and tools

A container (S4 class) for matrix-like assays

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

Add resources to ExperimentHub

Advanced analysis of microbial flow cytometry data

Affymetrix File Parsing SDK

Affymetrix GeneChip software compatibility

A fluent interface for manipulating GenomicRanges

A framework for rapid prototyping with file-based data structures

A generic R plugin dispatcher for BASE

AI and ML excursions with Bioconductor and tidymodels

A mass spectrometry imaging toolbox for statistical analysis

A matrix data storage object held in temporary files

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 Large Affymetrix Microarray Data Sets

analyze build artifacts for Bioconductor

Analyze, manage and store genomic data

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

An openCL compiler with the capacity to compile R functions and run the code on GPU

an R client for bedbase.org

An R Interface for Ribo Files

An R packaged zlib-1.2.5

'Antares' Results Processing

AnVILBilling

A package for importing and analyzing data from Roche's Genome Sequencer System

A package for secondary analysis of fusion products

A package to access the oncoKB web API

A package to search and retrieve data from Hub resources

A package with style requirements for the gDR suite

API access to Ocean Genomics txome.ai RNA-seq Analysis

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 simple search engine

Assertive Check Functions

A Tidy Implementation of Heatmap

A Tool for Integration of Big Bio Data

A unified framework for working transparently with on-disk and in-memory array-like datasets

Base Classes for Storing Genomic Interaction Data

Base Functions and Classes for Mass Spectrometry and Proteomics

Base Functions for Bioinformatics

Basic graphic utilities for visualization of genomic data.

Basilisk Installation Utilities

Bcbio Base Functions

Biobase: Base functions for Bioconductor

BiocCaseStudies: Support for the Case Studies Monograph

Bioconductor Algorithms for Big Data

Bioconductor Extensions for R Code Analysis Tools

Bioconductor facilities for parallel evaluation

Bioconductor on the AnVIL compute environment

Bioconductor Quality Enhancement

Bioconductor software ecosystem building tools

Bioconductor-specific package checks

Bioconductor Web Interface

biodb, a library and a development framework for connecting to chemical and biological databases

biodbChebi, a library for connecting to the ChEBI Database

biodbExpasy, a library for connecting to Expasy ENZYME database.

biodbHmdb, a library for connecting to the HMDB Database

biodbKegg, a library for connecting to the KEGG Database

biodbLipidmaps, a library for connecting to the Lipidmaps Structure database

biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database

biodbUniprot, a library for connecting to the Uniprot Database

Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful

Brings Seurat to the Tidyverse

Brings SingleCellExperiment to the Tidyverse

Brings SummarizedExperiment to the Tidyverse

Brings transcriptomics to the tidyverse

Build R / Bioconductor package binaries using Kubernetes on a cloud service

Bump Hunter

Bumpy Matrix of Non-Scalar Objects

Categorized views of R package repositories

cell counter

CGHbase: Base functions and classes for arrayCGH data analysis.

Challenges for the Bioconductor community

C++ headers and static libraries of Protocol buffers

Cheminformatics Toolkit for R

Classes and Methods for Handling Genomic Interaction Data

Classes and methods for performing benchmark comparisons

Classes for high-throughput arrays supported by oligo and crlmm

Class Unions, Matrix Operations, and Color Schemes for OOMPA

Client to access AnnotationHub resources

Client to access ExperimentHub resources

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

Coerce 'Actigraphy' to Summarized Experiments

Coercion methods for biological data

Collection of simple tools for learning about Bioconductor Packages

Collection of simple tools for learning about Bioc Packages

Collection of utility functions to work with .gda files in R

Compiling Bioconductor to Handle Each Matrix Type

Construct Benchmarks for Single Cell Analysis Methods

Container for PhIP-Seq Experiments

Convenience functions for adding packages to the svn repository

Convenience functions for adding packages to the svn repository.

Conveniently access PyRanges functionalities from Bioconductor

Conveniently import and query gene models

Convert Microarray Data Objects

Core Utils for Mass Spectrometry Data

Core Utils for Metabolomics Data

Create an ALTREP object by defining ALTREP functions in R

Create and Manager a Database specifically for Bioconductor build report statuses

Creates an interactive tcltk widget

Creating R Connection with Google Cloud Storage

Cross-target analysis of small molecule bioactivity

Data and code resources for microsatellite instability studies

Data and functions for dealing with microRNAs

Data Management API for epiviz interactive visualization app

Data management of large-scale whole-genome sequence variant calls

Data Management of Large-Scale Whole-Genome Sequence Variant Calls

DBI to construct LRBase-related package

DBI to construct MeSH-related package from sqlite file

DBI to construct MSEA-related package

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

Delayed operation on DataFrame using standard DataFrame metaphor

Detecting patterns of post-transcriptional modifications using machine learning

Detection of post-transcriptional modifications in high throughput sequencing data

Differential Coverage package

Direct Access to Orbitrap Data and Beyond

Display heatmap at different resolution level of a tree

Displaying binary trees with focus on dendrogram leaves

Distributed computing by file or by range

doseLM

doseR

Dynamic document tools

Effective mobility scale transformation of CE-MS(/MS) data

Efficient graph representation and manipulation in Bioconductor

Efficient manipulation of biological strings

Enabling stream processing of large files

Epiviz Genome Browser panel for iSEEu

Equality of 2 (or k) Continuous Univariate and Multivariate Distributions

Exploration of marker-gene sequence taxonomic annotations

Exploratory Systems Analysis Tools

explore metrics for sample annotation for genomic experiments

Exposes and makes available data from the cBioPortal web resources

Exposes and Makes Available Data from the cBioPortal Web Resources

Exposome exploration and outcome data analysis

Extract and manage matrix data from the Human Cell Atlas project

Facilities for Filtering Bioconductor Annotation Resources

File-System Toolbox for RAVE Project

Find/fix old serialized S4 instances

flowBeads: Analysis of flow bead data

flowCore: Basic structures for flow cytometry data

FlowRepository R Interface

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

Framework for Storing and Accessing Hi-C Data Through HDF Files

Freezing Python Dependencies Inside Bioconductor Packages

'fst' backend for DelayedArray objects

Functionality for Mass Spectrometry Features

Functionality Visualization for Motifs

Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects

Further Utilities for Genomic Interactions

General utility functions for developing Bioconductor packages

Generation of cell pictures

Generic and Biological Sequences

Generic infrastructure for Bioconductor mass spectrometry packages

Genometric Correlation package

GenoMetric Query Language for R/Bioconductor

GenomicOperations

Genomic Visualizations in R

GGBase infrastructure for genetics of gene expression package GGtools

Handling and Managing Peptide Spectrum Matches

HDF5 backend for DelayedArray objects

HDF5 Compression Filters

HDF5 datasets as array-like objects in R

HDF5 Delayed Array for Nifti Objects

HDF5 interface to R

hdf5 library as an R package

helpers for comprehension of S4

Higher-Order Deconvolution Survival Analyses

High-Level Data Analysis and Manipulation in 'tidyverse' Style

High-performance sparse data representation and manipulation in R

High-resolution exploration of SRA metadata and RNA-seq in AnVIL

High throughput prioritized acquisition and processing of tandem mass spectra

High-Throughput Sequence Analysis using the Aroma Framework

HMMRATAC - a semi-supervised machine learning approach for identifying open chromatin regions from ATAC-Seq data using Hidden Markov Models

Identifying Protein Binding Sites in High-Throughput Sequencing Data

Implementation of the dot bracket annotations with Biostrings

Import, Manipulate and Explore the Results of an 'Antares' Simulation

Import methods for 10X Genomics files

Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

Infrastructure for Biostrings-based genome data packages

Infrastructure for Chromatographic Mass Spectrometry Data

Infrastructure for Ion Mobility enabled mass spectrometry

Infrastructure for Mass Spectrometry Experiments

Infrastructure to work with genomewide position-specific scores

Install/Update Bioconductor and CRAN Packages

Install/Update Bioconductor, CRAN, and github Packages

Integrated Interpretation of Genes

Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

Integrating Spectra with Python's matchms

Interactive analysis of repeat elements

Interactively Gate Points

Interactive visualization and manipulation of nested networks

Interactive Visualization for Genomic Features

Interface for Popular Multiple Sequence Alignment Tools

interface to python sklearn via Rstudio reticulate

Interface to terra-notebook-utils

Interface to the RDP Classifier

Investigates Allele Specific Expression

Investigation of Fragmentation Conditions in Top-Down Proteomics

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

Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

LoomExperiment container

Make an R function available in the Galaxy web platform

Manages subsets of data with Bioconductor Experiment objects

Managing Expiration for Cache Directories

Manipulate Zarr archives as R objects

Manipulating and exploring protein and proteomics data

MassQL support for Spectra

Mass spectrometry data backend

Mass spectrometry Data Backend for Bruker TimsTOF Files

Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files

Mass Spectrometry Data Backend for MassBank record Files

Mass Spectrometry Data Backend for NIST msp Files

Mass spectrometry data backends for The Human Metabolome Database

Methods for accessing online The Cancer Genome Atlas (TCGA) data

Methods for reading CNAG files

Methods for reading dChip files

Methods for Reading dChip Files

Methods that apply to rows and columns of a matrix

Microarray Data related methods that utlize BufferedMatrix objects

mimager: The Microarray Imager

Mismatch Tolerant Maximum Common Substructure Searching

Model-View-Controller (MVC) Classes

Model-View-Controller (MVC) Classes That Use Biobase

Mounting a Google Cloud bucket to a local directory

multivariate outlier detection for expression array QA

Munich ChronoType Questionnaire Tools

Network-based prioritization of putative metabolite IDs

NPMLE for Censored and Truncated Data

Object design (S4) for AMARETTO

Objective Assessment of Copy-Number Estimates

OpenAccess TCGA Data on Terra as MultiAssayExperiment

Open-source toolkit to analyse data from xCELLigence System (RTCA)

Operations on genomic intervals

Optional Type Specification Prototype

Out-of-core statistical computing and signal processing

Package Dependency Tools

Package for CTDbase data query, visualization and downstream analysis

package range tools

Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)

parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)

parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

Parsing GenBank files into semantically useful objects

Parsing Illumina Microarray Output Files

Phenotyping of microbial Raman spectroscopy data

Pipeline framework for bioinformatics in R

Pipette Biological Data In and Out of R

Platform Design Information Package Builder

Post-normalization of total copy numbers

Presence-Absence Calls from Negative Strand Matching Probesets

Process Incucyte Growth Curve Data

processing of ontologies of anatomy, cell lines, and so on

Provide a 'redis' back-end for BiocParallel

Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).

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

Publish Packages and Other Resources to AnVIL Workspaces

Quality control and standardization of cytometry data

Quality control for flow cytometry

Quality Control of Gated Flow Cytometry Experiments

Quality Control of Protemics Data

Quantitative features for mass spectrometry data

Query the gene models of a given organism/assembly

R based tk widgets

RBDmap

R bindings for cytolib c++ library

R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations

Reorganization of rhdf5client code

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 and manipulation of short genomic alignments

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

Reusable and reproducible Data Management

Re-using Content in Bioconductor Books

RIC (RNA interaction capture)

R interface to a subset of OpenBabel functionalities

R Interface to CoreArray Genomic Data Structure (GDS) Files

R interface to EBI MGnify metagenomics resource

R Interface to epiviz web app

R Interface to HDF5

R interface to PSI-MI 2.5 files

R Interface to the metaviz web app for interactive metagenomics data analysis and visualization

R interface to the pepXML standard

R Interface to UniProt Web Services

RNASeq2GeneNorm assays in HDF Scalable Data Service for five TCGA tumors

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

R objects for common work flow language representation

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

R Package Template - Enhanced

R package using github actions to determine dependencies of a given package.

R SDK for BaseSpace RESTful API

R SeqAn

Run Epiviz Interactive Genomic Data Visualization App within R

Run workflows implemented in Terra/AnVIL workspace

R utilities for rabix.

S4 Classes for Single Cell Data

S4 Class for Spatial Experiments handling

S4 Class for Spatially Resolved -omics Data

S4 generic functions for Bioconductor

S4 generic functions for Bioconductor proteomics infrastructure

S4 generic functions used in Bioconductor

S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects

S4 implementation of vector-like and list-like objects

Set the appropriate version of Bioconductor packages

Sharing R objects across multiple R processes without memory duplication

Similarity measures for chemical compounds

Simple Demo of S4 Methods and Classes for Bioconductor

simple interfaces from OpenCRAVAT to Bioconductor

Simulation of ChIP-seq experiments

Single-cell analysis toolkit for gene expression data in R

Single-Cell Analysis Toolkit for Gene Expression Data in R

Software for the integration of multi-omics experiments in Bioconductor

Software infrastructure for efficient representation of full genomes and their SNPs

Software to enable the smooth interfacing of different database packages

Spatial Transcriptomics Analysis

Spectra Infrastructure for Mass Spectrometry Data

Spectrum Infrastructure for Mass Spectrometry Data

splicegear

spsBio: A systemPipeShiny plugin for biological data visualization

SQL-based Mass Spectrometry Data Backend

Statistical analysis of hydrogen deuterium exchange mass spectrometry

Statistical Interpretation of Heatmaps

Statistical tools and data structures for plate-based flow cytometry

structured corruption of affymetrix cel file data

Submitter and Monitor of the 'LSF Cluster'

SummarizedExperiment container

Summary Statistics for Rows and Columns of Sparse Matrices

support for build system

Support package for GenomicFeatures

Symphony integer linear programming solver in R

Synchronious locking mechanisms

Syntactically Valid Names

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: Workflow Environment for Data Analysis and Report Generation

systemPipeShiny: An Interactive Framework for Workflow Management and Visualization

Test package: Base functions for Bioconductor

text mining for msigdb sets construed as documents

The Herper package is a simple toolset to install and manage conda packages and environments from R

Tools and extensions for processing Sweave documents

Tools for Actigraphy Data Analysis

Tools for building SNPlocs data packages

Tools for building SQLite-based annotation data packages

Tools for data visualization

Tools for parsing Affymetrix data files

Tools for preparing an ImmPort Data Submission

Tools for visualizing genomics data

Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells

Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells.

Tools to Process the Munich ChronoType Questionnaire (MCTQ)

Tools to work with a Compendium of 181000 human transcriptome sequencing studies

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

Transcription Factors Association Rules Miner

TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

Use pyAnVIL and SMART infrastructure to work with AnVIL FHIR in R

use REST API to write data to HDF Cloud

Using TileDB as a DelayedArray Backend

Utilities for Annotation of Metabolomics Data

utilities for exploration of human metabolome database

Utilities for flow cytometry

Utilities for handling genomic interaction data

Utilities to create and use Bioconductor Hubs

Utility Functions from the Eurac Research Computational Metabolomics Team

vdummy

Visualization for flow cytometry

Visualization tools for gene fusions

Visualization tools for genomic data

Visualize Cytometry data with ggplot

WebSocket server infrastructure for epivizr apps and packages

What the package does (short line)

Working with Illumina Basecalling and Demultiplexing input and output files

Working with modified nucleotide sequences

Zwyx

Biocview "Infrastructure"

R Package Documentation

Browse R Packages

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