Biocview "Infrastructure"

Accelerated similarity searching of small molecules
Accelerated similarity searching of small molecules
Accelerated similarity searching of small molecules
Access Bioconductor docker images
Access Bioconductor docker images
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
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 ENCODE metadata
A compilation of ENCODE metadata
A compilation of metadata from NCBI GEO
A compilation of metadata from NCBI GEO
A compilation of metadata from NCBI GEO
A compilation of metadata from NCBI SRA and tools
A compilation of metadata from NCBI SRA and tools
A compilation of metadata from NCBI SRA and tools
Add resources to ExperimentHub
Add resources to ExperimentHub
Advanced analysis of microbial flow cytometry data
Affymetrix File Parsing SDK
Affymetrix File Parsing SDK
Affymetrix GeneChip software compatibility
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 generic R plugin dispatcher for BASE
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
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 Large Affymetrix Microarray Data Sets
Analysis of Large Affymetrix Microarray Data Sets
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 openCL compiler with the capacity to compile R functions and run the code on GPU
An R Interface for Ribo Files
An R Interface for Ribo Files
An R packaged zlib-1.2.5
'Antares' Results Processing
'Antares' Results Processing
A package for importing and analyzing data from Roche's Genome Sequencer System
A package for secondary analysis of fusion products
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 set of annotation maps describing the entire PANTHER Gene Ontology
a simple search engine
a simple search engine
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
A unified framework for working transparently with on-disk and in-memory array-like datasets
Base Classes for Storing Genomic Interaction Data
Base Classes for Storing Genomic Interaction Data
Base Functions and Classes for Mass Spectrometry and Proteomics
Base Functions and Classes for Mass Spectrometry and Proteomics
Basic graphic utilities for visualization of genomic data.
Basic graphic utilities for visualization of genomic data.
Basilisk Installation Utilities
Basilisk Installation Utilities
bcbio Base Functions
Biobase: Base functions for Bioconductor
Biobase: Base functions for Bioconductor
BiocCaseStudies: Support for the Case Studies Monograph
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 facilities for parallel evaluation
Bioconductor on the AnVIL compute environment
Bioconductor on the AnVIL compute environment
Bioconductor-specific package checks
Bioconductor-specific package checks
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
biodbHmdb, a library for connecting to the HMDB Database
biodbKegg, a library for connecting to the KEGG Database
biodbUniprot, a library for connecting to the Uniprot Database
Brings transcriptomics to the tidyverse
Bump Hunter
Bump Hunter
Bump Hunter
Categorized views of R package repositories
Categorized views of R package repositories
cell counter
CGHbase: Base functions and classes for arrayCGH data analysis.
CGHbase: Base functions and classes for arrayCGH data analysis.
C++ headers and static libraries of Protocol buffers
C++ headers and static libraries of Protocol buffers
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Classes and Methods for Handling Genomic Interaction Data
Classes and methods for performing benchmark comparisons
Classes and methods for performing benchmark comparisons
Classes for high-throughput arrays supported by oligo and crlmm
Classes for high-throughput arrays supported by oligo and crlmm
Classes for high-throughput arrays supported by oligo and crlmm
Classes for high-throughput arrays supported by oligo and crlmm
Class Unions, Matrix Operations, and Color Schemes for OOMPA
Class Unions, Matrix Operations, and Color Schemes for OOMPA
Client to access AnnotationHub resources
Client to access AnnotationHub resources
Client to access ExperimentHub resources
Client to access ExperimentHub resources
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Coercion methods for biological data
Coercion methods for biological data
Coercion methods for biological data
Collection of simple tools for learning about Bioc Packages
Collection of simple tools for learning about Bioc 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
Compiling Bioconductor to Handle Each Matrix Type
Construct Benchmarks for Single Cell Analysis Methods
Construct Benchmarks for Single Cell Analysis Methods
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
Conveniently import and query gene models
Convert Microarray Data Objects
Core Utils for Mass Spectrometry Data
Core Utils for Mass Spectrometry Data
Core Utils for Metabolomics Data
Create an ALTREP object by defining ALTREP functions in R
Creates an interactive tcltk widget
Creating R Connection with Google Cloud Storage
Creating R Connection with Google Cloud Storage
Cross-target analysis of small molecule bioactivity
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 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 LRBase-related package
DBI to construct MeSH-related package from sqlite file
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
Detecting patterns of post-transcriptional modifications using machine learning
Detecting patterns of post-transcriptional modifications using machine learning
Detection of post-transcriptional modifications in high throughput sequencing data
Detection of post-transcriptional modifications in high throughput sequencing data
Differential Coverage package
Display heatmap at different resolution level of a tree
Distributed computing by file or by range
Distributed computing by file or by range
doseLM
doseR
doseR
doseR
doseR
doseR
doseR
Dynamic document tools
Dynamic document tools
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
Enabling stream processing of large files
Exploration of marker-gene sequence taxonomic annotations
Exploration of marker-gene sequence taxonomic annotations
Exploratory Systems Analysis Tools
explore metrics for sample annotation for genomic experiments
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
Exposes and makes available data from the cBioPortal web resources
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
Facilities for Filtering Bioconductor Annotation Resources
Facilities for Filtering Bioconductor Annotation Resources
Facilities for Filtering Bioconductor Annotation Resources
Facilities for Filtering Bioconductor Annotation Resources
flowBeads: Analysis of flow bead data
flowBeads: Analysis of flow bead data
flowCore: Basic structures for flow cytometry data
flowCore: Basic structures for flow cytometry data
FlowRepository R Interface
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
Framework for Storing and Accessing Hi-C Data Through HDF Files
Framework for Storing and Accessing Hi-C Data Through HDF Files
Framework for Storing and Accessing Hi-C Data Through HDF Files
Framework for Storing and Accessing Hi-C Data Through HDF Files
Freezing Python Dependencies Inside Bioconductor Packages
Freezing Python Dependencies Inside Bioconductor Packages
Freezing Python Versions Inside Bioconductor Packages
Friendly tidy wrappers for streamlined bulk transcriptional analysis
Friendly tidy wrappers for streamlined bulk transcriptional analysis
Friendly tidy wrappers for streamlined bulk transcriptional analysis
'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
Generic and Biological Sequences
Generic and Biological Sequences
Genometric Correlation package
GenoMetric Query Language for R/Bioconductor
GenoMetric Query Language for R/Bioconductor
GenomicOperations
GenomicOperations
Genomic Visualizations in R
Genomic Visualizations in R
GGBase infrastructure for genetics of gene expression package GGtools
HDF5 backend for DelayedArray objects
HDF5 backend for DelayedArray objects
HDF5 Compression Filters
HDF5 Delayed Array for Nifti Objects
HDF5 Delayed Array for Nifti Objects
HDF5 Delayed Array for Nifti Objects
HDF5 Delayed Array for Nifti Objects
HDF5 interface to R
hdf5 library as an R package
hdf5 library as an R package
helpers for comprehension of S4
High-Level Data Analysis and Manipulation in 'tidyverse' Style
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
Implementation of the dot bracket annotations with Biostrings
Import, Manipulate and Explore the Results of an 'Antares' Simulation
Import, Manipulate and Explore the Results of an 'Antares' Simulation
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 representation of Mass Spectrometry Data
Infrastructure for Mass Spectrometry Experiments
Infrastructure to work with genomewide position-specific scores
Infrastructure to work with genomewide position-specific scores
Install/Update Bioconductor and CRAN Packages
Install/Update Bioconductor, CRAN, and github 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 Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
Interactive analysis of repeat elements
Interactive visualization and manipulation of nested networks
Interactive Visualization for Genomic Features
Interactive Visualization for Genomic Features
Interface for Popular Multiple Sequence Alignment Tools
interface to python sklearn via Rstudio reticulate
interface to python sklearn via Rstudio reticulate
interface to python sklearn via Rstudio reticulate
Interface to the Basic Local Alignment Search Tool (BLAST)
Interface to the RDP Classifier
Investigates Allele Specific Expression
Investigates Allele Specific Expression
Investigation of Fragmentation Conditions in Top-Down Proteomics
Investigation of Fragmentation Conditions in Top-Down Proteomics
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
LoomExperiment container
LoomExperiment container
Make an R function available in the Galaxy web platform
Make an R function available in the Galaxy web platform
Make an R function available in the Galaxy web platform
Make an R function available in the Galaxy web platform
Make an R function available in the Galaxy web platform
Manipulate Zarr archives as R objects
Manipulating and exploring protein and proteomics data
Manipulating and exploring protein and proteomics data
Mass spectrometry data backend
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
Mass spectrometry data backends for The Human Metabolome Database
Methods for accessing online The Cancer Genome Atlas (TCGA) data
Methods for accessing online The Cancer Genome Atlas (TCGA) data
Methods for reading CNAG files
Methods for reading CNAG files
Methods for reading dChip 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
mimager: The Microarray Imager
Mismatch Tolerant Maximum Common Substructure Searching
Mismatch Tolerant Maximum Common Substructure Searching
Mismatch Tolerant Maximum Common Substructure Searching
Model-View-Controller (MVC) Classes
Model-View-Controller (MVC) Classes That Use Biobase
multivariate outlier detection for expression array QA
Network-based prioritization of putative metabolite IDs
Network-based prioritization of putative metabolite IDs
Network-based prioritization of putative metabolite IDs
NPMLE for Censored and Truncated Data
NPMLE for Censored and Truncated Data
Object design (S4) for AMARETTO
Objective Assessment of Copy-Number Estimates
Open-source toolkit to analyse data from xCELLigence System (RTCA)
Operations on genomic intervals
Optional Type Specification Prototype
Package Dependency Tools
Package Dependency Tools
Package for CTDbase data query, visualization and downstream analysis
Package for CTDbase data query, visualization and downstream analysis
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
parser for netCDF, mzXML, mzData 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 GenBank files into semantically useful objects
Parsing Illumina Microarray Output Files
Parsing Illumina Microarray Output Files
Phenotyping of microbial Raman spectroscopy data
Pipeline framework for bioinformatics in R
Pipeline framework for bioinformatics in R
Platform Design Information Package Builder
Platform Design Information Package Builder
Platform Design Information Package Builder
Platform Design Information Package Builder
Post-normalization of total copy numbers
Post-normalization of total copy numbers
Presence-Absence Calls from Negative Strand Matching Probesets
processing of ontologies of anatomy, cell lines, and so on
processing of ontologies of anatomy, cell lines, and so on
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
Quality control and standardization of cytometry data
Quality control for flow cytometry
Quality Control of Gated Flow Cytometry Experiments
Quantitative features for mass spectrometry data
Quantitative features for mass spectrometry data
R based tk widgets
RBDmap
R bindings for cytolib c++ library
R/Bioconductor package to manage hierarchies in genomic datasets
R/Bioconductor package to manage hierarchies in genomic datasets
Reorganization of rhdf5client code
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 and manipulation of short genomic alignments
Representation and manipulation of short genomic alignments
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 interface to a subset of OpenBabel functionalities
R interface to a subset of OpenBabel functionalities
R Interface to CoreArray Genomic Data Structure (GDS) Files
R Interface to CoreArray Genomic Data Structure (GDS) Files
R Interface to epiviz web app
R Interface to epiviz web app
R Interface to epiviz web app
R Interface to epiviz web app
R Interface to HDF5
R interface to PSI-MI 2.5 files
R interface to PSI-MI 2.5 files
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 metaviz web app for interactive metagenomics data analysis and visualization
R interface to the pepXML standard
R interface to the pepXML standard
R Interface to UniProt Web Services
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
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
R objects for common work flow language representation
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 Epiviz Interactive Genomic Data Visualization App within R
R utilities for rabix.
S4 Classes for Single Cell Data
S4 Classes for Single Cell Data
S4 Classes for Single Cell Data
S4 generic functions for Bioconductor
S4 generic functions for Bioconductor proteomics infrastructure
S4 generic functions for Bioconductor proteomics infrastructure
S4 generic functions used in Bioconductor
S4 generic functions used in Bioconductor
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
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
Set the appropriate version of Bioconductor packages
Sharing R objects across multiple R processes without memory duplication
Sharing R objects across multiple R processes without memory duplication
Similarity measures for chemical compounds
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
Single-Cell Analysis Toolkit for Gene Expression Data in R
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
Software to enable the smooth interfacing of different database packages
Software to enable the smooth interfacing of different database packages
Spatial Transcriptomics Analysis
Spatial Transcriptomics Analysis
Spectra Infrastructure for Mass Spectrometry Data
Spectra Infrastructure for Mass Spectrometry Data
Spectrum Infrastructure for Mass Spectrometry Data
splicegear
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
SummarizedExperiment container
SummarizedExperiment container
Summary Statistics for Rows and Columns of Sparse Matrices
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
systemPipeRdata: NGS workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: NGS workflow and report generation environment
text mining for msigdb sets construed as documents
Tools and extensions for processing Sweave documents
Tools for building SQLite-based annotation data packages
Tools for building SQLite-based annotation data packages
Tools for parsing Affymetrix data files
Tools for preparing an ImmPort Data Submission
Tools for preparing an ImmPort Data Submission
Tools for visualizing genomics data
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 analyze in vivo microscopy imaging data focused on tracking flowing blood cells.
Tools to work with a Compendium of 181000 human transcriptome sequencing studies
Tools to work with a Compendium of 181000 human transcriptome sequencing studies
Transcription Factors Association Rules Miner
Transcription Factors Association Rules Miner
Transcription Factors Association Rules Miner
TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
use REST API to write data to HDF Cloud
utilities for exploration of human metabolome database
utilities for exploration of human metabolome database
Utilities for flow cytometry
Utilities for flow cytometry
Utilities for handling genomic interaction data
Utilities for handling genomic interaction data
Utilities for handling genomic interaction data
Utility Functions from the Eurac Research Computational Metabolomics Team
Visualization for flow cytometry
Visualization tools for gene fusions
Visualization tools for gene fusions
Visualization tools for genomic data
Visualization tools for genomic data
Visualize Cytometry data with ggplot
Visualize Cytometry data with ggplot
WebSocket server infrastructure for epivizr apps and packages
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 Illumina Basecalling and Demultiplexing input and output files
Working with modified nucleotide sequences
Working with modified nucleotide sequences
Zwyx