Data

Tools

Indexes

Applications

Experiments

Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

bioconductor.org "Infrastructure" keyword

Top 1.1% on bioconductor.org
BiocParallel 1.44.0
Bioconductor facilities for parallel evaluation
10 versions - Latest release: 4 months ago - 377 dependent packages - 8.77 million downloads total - 63 stars on GitHub - 1 maintainer
Top 0.8% on bioconductor.org
BSgenome 1.78.0
Software infrastructure for efficient representation of full genomes and their SNPs
8 versions - Latest release: 4 months ago - 129 dependent packages - 2.8 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
GenomicRanges 1.62.1
Representation and manipulation of genomic intervals
10 versions - Latest release: 3 months ago - 604 dependent packages - 9.32 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
S4Vectors 0.48.0
Foundation of vector-like and list-like containers in Bioconductor
9 versions - Latest release: 4 months ago - 740 dependent packages - 11.2 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
HDF5Array 1.38.0
HDF5 datasets as array-like objects in R
8 versions - Latest release: 4 months ago - 54 dependent packages - 1.74 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
XVector 0.50.0
Foundation of external vector representation and manipulation in Bioconductor
6 versions - Latest release: 4 months ago - 36 dependent packages - 9.46 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
SingleCellExperiment 1.32.0
S4 Classes for Single Cell Data
8 versions - Latest release: 4 months ago - 201 dependent packages - 2.03 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
DelayedArray 0.36.0
A unified framework for working transparently with on-disk and in-memory array-like datasets
8 versions - Latest release: 4 months ago - 111 dependent packages - 7.81 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
GenomicFeatures 1.62.0
Query the gene models of a given organism/assembly
9 versions - Latest release: 4 months ago - 183 dependent packages - 4.3 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
Biobase 2.70.0
Biobase: Base functions for Bioconductor
6 versions - Latest release: 4 months ago - 518 dependent packages - 11.2 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
IRanges 2.44.0
Foundation of integer range manipulation in Bioconductor
8 versions - Latest release: 4 months ago - 563 dependent packages - 11.7 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.78.0
Efficient manipulation of biological strings
11 versions - Latest release: 4 months ago - 333 dependent packages - 9.4 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
MSnbase 2.36.0
Base Functions and Classes for Mass Spectrometry and Proteomics
8 versions - Latest release: 4 months ago - 30 dependent packages - 592 thousand downloads total - 123 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.54.1
R Interface to HDF5
11 versions - Latest release: 3 months ago - 69 dependent packages - 3.28 million downloads total - 72 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
GenomicAlignments 1.46.0
Representation and manipulation of short genomic alignments
8 versions - Latest release: 4 months ago - 132 dependent packages - 4.93 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.38.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
9 versions - Latest release: 4 months ago - 96 dependent packages - 1.06 million downloads total - 1 maintainer
Top 0.8% on bioconductor.org
flowCore 2.22.1
flowCore: Basic structures for flow cytometry data
9 versions - Latest release: about 2 months ago - 51 dependent packages - 4.95 million downloads total - 1 maintainer
Top 3.2% on bioconductor.org
lpsymphony 1.38.0
Symphony integer linear programming solver in R
6 versions - Latest release: 3 months ago - 1 dependent package - 201 thousand downloads total - 1 maintainer
rawrr 1.18.0
Direct Access to Orbitrap Data and Beyond
8 versions - Latest release: 4 months ago - 1 dependent package - 20 thousand downloads total - 57 stars on GitHub - 1 maintainer
Top 0.2% on bioconductor.org
SummarizedExperiment 1.40.0
A container (S4 class) for matrix-like assays
7 versions - Latest release: 4 months ago - 632 dependent packages - 7.72 million downloads total - 1 maintainer
AnVILPublish 1.20.0
Publish Packages and Other Resources to AnVIL Workspaces
6 versions - Latest release: 4 months ago - 10.1 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
oligoClasses 1.72.0
Classes for high-throughput arrays supported by oligo and crlmm
6 versions - Latest release: 4 months ago - 12 dependent packages - 441 thousand downloads total - 1 maintainer
BaseSpaceR 1.54.0
R SDK for BaseSpace RESTful API
6 versions - Latest release: 3 months ago - 33.1 thousand downloads total - 1 maintainer
Top 0.1% on bioconductor.org
BiocGenerics 0.56.0
S4 generic functions used in Bioconductor
7 versions - Latest release: 4 months ago - 729 dependent packages - 12 million downloads total - 1 maintainer
Top 8.3% on bioconductor.org
MVCClass 1.84.0
Model-View-Controller (MVC) Classes
6 versions - Latest release: 3 months ago - 1 dependent package - 40.8 thousand downloads total - 1 maintainer
Top 9.4% on bioconductor.org
R453Plus1Toolbox 1.60.0
A package for importing and analyzing data from Roche's Genome Sequencer System
7 versions - Latest release: about 1 month ago - 34.9 thousand downloads total - 1 maintainer
matter 2.12.0
Out-of-core statistical computing and signal processing
10 versions - Latest release: 4 months ago - 2 dependent packages - 37.7 thousand downloads total - 52 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
flowViz 1.74.0
Visualization for flow cytometry
6 versions - Latest release: 3 months ago - 11 dependent packages - 369 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
DelayedMatrixStats 1.32.0
Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
7 versions - Latest release: 4 months ago - 45 dependent packages - 1.95 million downloads total - 15 stars on GitHub - 1 maintainer
gDRimport 1.8.1
Package for handling the import of dose-response data
7 versions - Latest release: 2 months ago - 2 dependent packages - 7.13 thousand downloads total - 3 stars on GitHub - 1 maintainer
CellBench 1.26.0
Construct Benchmarks for Single Cell Analysis Methods
6 versions - Latest release: 4 months ago - 2 dependent packages - 17.8 thousand downloads total - 32 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
ProtGenerics 1.42.0
Generic infrastructure for Bioconductor mass spectrometry packages
6 versions - Latest release: 4 months ago - 20 dependent packages - 1.53 million downloads total - 7 stars on GitHub - 1 maintainer
ssrch 1.26.0
a simple search engine
6 versions - Latest release: 3 months ago - 1 dependent package - 11.8 thousand downloads total - 1 maintainer
h5mread 1.2.1
A fast HDF5 reader
3 versions - Latest release: 3 months ago - 191 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
OrganismDbi 1.52.0
Software to enable the smooth interfacing of different database packages
6 versions - Latest release: 3 months ago - 6 dependent packages - 585 thousand downloads total - 1 maintainer
UCSC.utils 1.6.1
Low-level utilities to retrieve data from the UCSC Genome Browser
5 versions - Latest release: 2 months ago - 2 dependent packages - 1.43 million downloads total - 1 maintainer
tidySummarizedExperiment 1.20.1
Brings SummarizedExperiment to the Tidyverse
7 versions - Latest release: 3 months ago - 5 dependent packages - 24.1 thousand downloads total - 26 stars on GitHub - 1 maintainer
ExperimentSubset 1.20.0
Manages subsets of data with Bioconductor Experiment objects
7 versions - Latest release: 3 months ago - 10.4 thousand downloads total - 1 maintainer
QTLExperiment 2.2.0
S4 classes for QTL summary statistics and metadata
5 versions - Latest release: 4 months ago - 1 dependent package - 6.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
basilisk.utils 1.22.0
Centralized Conda Installation for Bioconductor Packages
7 versions - Latest release: 4 months ago - 2 dependent packages - 267 thousand downloads total - 1 maintainer
TFARM 1.32.0
Transcription Factors Association Rules Miner
6 versions - Latest release: 3 months ago - 14.2 thousand downloads total - 1 maintainer
Cardinal 3.12.1
A mass spectrometry imaging toolbox for statistical analysis
12 versions - Latest release: 2 days ago - 46.3 thousand downloads total - 1 maintainer
Top 10.0% on bioconductor.org
BioMVCClass 1.78.0
Model-View-Controller (MVC) Classes That Use Biobase
6 versions - Latest release: 4 months ago - 43.6 thousand downloads total - 1 maintainer
BiocSklearn 1.32.0
interface to python sklearn via Rstudio reticulate
7 versions - Latest release: 3 months ago - 24.5 thousand downloads total - 1 maintainer
systemPipeShiny 1.20.0
systemPipeShiny: An Interactive Framework for Workflow Management and Visualization
6 versions - Latest release: 4 months ago - 10.9 thousand downloads total - 1 maintainer
Streamer 1.56.0
Enabling stream processing of large files
6 versions - Latest release: 3 months ago - 31 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
TreeSummarizedExperiment 2.18.0
TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
7 versions - Latest release: 4 months ago - 13 dependent packages - 156 thousand downloads total - 1 maintainer
scTreeViz 1.16.0
R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with h...
7 versions - Latest release: 3 months ago - 8.45 thousand downloads total - 1 maintainer
BumpyMatrix 1.18.0
Bumpy Matrix of Non-Scalar Objects
6 versions - Latest release: 3 months ago - 10 dependent packages - 54.1 thousand downloads total - 1 maintainer
MsBackendMsp 1.14.0
Mass Spectrometry Data Backend for NIST msp Files
6 versions - Latest release: 4 months ago - 18.4 thousand downloads total - 5 stars on GitHub - 1 maintainer
BiocBook 1.8.0
Write, containerize, publish and version Quarto books with Bioconductor
5 versions - Latest release: 3 months ago - 6.55 thousand downloads total - 1 maintainer
shinybiocloader 1.0.0
Use a Shiny Bioconductor CSS loader
1 version - Latest release: 4 months ago - 1.12 thousand downloads total - 1 maintainer
Top 3.7% on bioconductor.org
InteractionSet 1.38.0
Base Classes for Storing Genomic Interaction Data
7 versions - Latest release: 3 months ago - 23 dependent packages - 203 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
AnnotationForge 1.52.0
Tools for building SQLite-based annotation data packages
6 versions - Latest release: 3 months ago - 5 dependent packages - 596 thousand downloads total - 1 maintainer
epivizrServer 1.38.0
WebSocket server infrastructure for epivizr apps and packages
6 versions - Latest release: 3 months ago - 5 dependent packages - 23.3 thousand downloads total - 1 maintainer
Top 9.4% on bioconductor.org
RTCA 1.62.0
Open-source toolkit to analyse data from xCELLigence System (RTCA)
6 versions - Latest release: 3 months ago - 34 thousand downloads total - 1 maintainer
MsExperiment 1.12.0
Infrastructure for Mass Spectrometry Experiments
7 versions - Latest release: 3 months ago - 2 dependent packages - 63.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
AnVILAz 1.4.0
R / Bioconductor Support for the AnVIL Azure Platform
3 versions - Latest release: 4 months ago - 4.07 thousand downloads total - 0 stars on GitHub - 1 maintainer
VCFArray 1.26.0
Representing on-disk / remote VCF files as array-like objects
6 versions - Latest release: 4 months ago - 12.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
iSEEhex 1.12.0
iSEE extension for summarising data points in hexagonal bins
6 versions - Latest release: 4 months ago - 1 dependent package - 9.85 thousand downloads total - 0 stars on GitHub - 1 maintainer
rebook 1.20.0
Re-using Content in Bioconductor Books
6 versions - Latest release: 3 months ago - 16.1 thousand downloads total - 1 maintainer
Top 5.9% on bioconductor.org
systemPipeR 2.16.3
systemPipeR: Workflow Environment for Data Analysis and Report Generation
8 versions - Latest release: about 1 month ago - 3 dependent packages - 279 thousand downloads total - 54 stars on GitHub - 1 maintainer
AnVILBilling 1.20.0
Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).
6 versions - Latest release: 3 months ago - 9.43 thousand downloads total - 0 stars on GitHub - 1 maintainer
VariantExperiment 1.24.0
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
7 versions - Latest release: 4 months ago - 9.96 thousand downloads total - 1 stars on GitHub - 1 maintainer
ribor 1.22.0
An R Interface for Ribo Files
6 versions - Latest release: 3 months ago - 10.5 thousand downloads total - 1 maintainer
chimeraviz 1.36.0
Visualization tools for gene fusions
6 versions - Latest release: 4 months ago - 24.8 thousand downloads total - 38 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
biocViews 1.78.0
Categorized views of R package repositories
6 versions - Latest release: 3 months ago - 8 dependent packages - 635 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
DynDoc 1.88.0
Dynamic document tools
6 versions - Latest release: 4 months ago - 1 dependent package - 472 thousand downloads total - 1 maintainer
tidybulk 2.0.1
Brings transcriptomics to the tidyverse
8 versions - Latest release: 4 months ago - 1 dependent package - 25.8 thousand downloads total - 176 stars on GitHub - 1 maintainer
SRAdb 1.72.0
A compilation of metadata from NCBI SRA and tools
7 versions - Latest release: 3 months ago - 135 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
affyio 1.80.0
Tools for parsing Affymetrix data files
6 versions - Latest release: 3 months ago - 12 dependent packages - 1.92 million downloads total - 3 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
aroma.light 3.40.0
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Da...
6 versions - Latest release: 3 months ago - 3 dependent packages - 418 thousand downloads total - 1 stars on GitHub - 1 maintainer
GCPtools 1.0.0
Tools for working with gcloud and gsutil
1 version - Latest release: 4 months ago - 2.53 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
SNPRelate 1.44.0
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
8 versions - Latest release: 4 months ago - 11 dependent packages - 270 thousand downloads total - 108 stars on GitHub - 1 maintainer
SCArray 1.18.0
Large-scale single-cell omics data manipulation with GDS files
6 versions - Latest release: 4 months ago - 1 dependent package - 10.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
SpatialExperiment 1.20.0
S4 Class for Spatially Resolved -omics Data
7 versions - Latest release: 3 months ago - 36 dependent packages - 323 thousand downloads total - 54 stars on GitHub - 1 maintainer
rRDP 1.44.0
Interface to the RDP Classifier
6 versions - Latest release: 4 months ago - 21.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
updateObject 1.14.0
Find/fix old serialized S4 instances
6 versions - Latest release: 4 months ago - 6.84 thousand downloads total - 1 maintainer
LRBaseDbi 2.20.0
DBI to construct LRBase-related package
8 versions - Latest release: 3 months ago - 1 dependent package - 14.3 thousand downloads total - 1 maintainer
Top 8.6% on bioconductor.org
Spectra 1.20.1
Spectra Infrastructure for Mass Spectrometry Data
11 versions - Latest release: about 1 month ago - 15 dependent packages - 152 thousand downloads total - 43 stars on GitHub - 1 maintainer
MetID 1.28.0
Network-based prioritization of putative metabolite IDs
6 versions - Latest release: 4 months ago - 12.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
scviR 1.10.0
experimental inferface from R to scvi-tools
6 versions - Latest release: 3 months ago - 5.87 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
microRNA 1.68.0
Data and functions for dealing with microRNAs
6 versions - Latest release: 3 months ago - 1 dependent package - 105 thousand downloads total - 1 maintainer
Top 5.8% on bioconductor.org
GenomicScores 2.22.0
Infrastructure to work with genomewide position-specific scores
11 versions - Latest release: 3 months ago - 6 dependent packages - 88.8 thousand downloads total - 9 stars on GitHub - 1 maintainer
RNAmodR 1.24.0
Detection of post-transcriptional modifications in high throughput sequencing data
6 versions - Latest release: 3 months ago - 3 dependent packages - 13.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
TnT 1.32.0
Interactive Visualization for Genomic Features
7 versions - Latest release: 4 months ago - 14.6 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 6.2% on bioconductor.org
weaver 1.76.0
Tools and extensions for processing Sweave documents
6 versions - Latest release: 3 months ago - 45.6 thousand downloads total - 1 maintainer
BiocHail 1.10.0
basilisk and hail
7 versions - Latest release: 4 months ago - 4.56 thousand downloads total - 6 stars on GitHub - 1 maintainer
MultimodalExperiment 1.10.0
Integrative Bulk and Single-Cell Experiment Container
6 versions - Latest release: 3 months ago - 6.31 thousand downloads total - 1 maintainer
Top 1.0% on bioconductor.org
MatrixGenerics 1.22.0
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
7 versions - Latest release: 4 months ago - 45 dependent packages - 5.45 million downloads total - 1 maintainer
txdbmaker 1.6.2
Tools for making TxDb objects from genomic annotations
9 versions - Latest release: 2 months ago - 8 dependent packages - 175 thousand downloads total - 1 maintainer
beachmat.hdf5 1.8.0
beachmat bindings for HDF5-backed matrices
5 versions - Latest release: 3 months ago - 1 dependent package - 10.2 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
rhdf5filters 1.22.0
HDF5 Compression Filters
8 versions - Latest release: 4 months ago - 2 dependent packages - 2.17 million downloads total - 5 stars on GitHub - 1 maintainer
biodbHmdb 1.15.0
biodbHmdb, a library for connecting to the HMDB Database
7 versions - Latest release: 3 months ago - 7.65 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
CGHbase 1.70.0
CGHbase: Base functions and classes for arrayCGH data analysis.
6 versions - Latest release: 4 months ago - 6 dependent packages - 104 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.1% on bioconductor.org
MeSHDbi 1.46.0
DBI to construct MeSH-related package from sqlite file
6 versions - Latest release: 3 months ago - 3 dependent packages - 632 thousand downloads total - 1 maintainer
BiocBaseUtils 1.12.0
General utility functions for developing Bioconductor packages
6 versions - Latest release: 3 months ago - 11 dependent packages - 397 thousand downloads total - 4 stars on GitHub - 1 maintainer
xenLite 1.4.0
Simple classes and methods for managing Xenium datasets
4 versions - Latest release: 3 months ago - 3.36 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.8% on bioconductor.org
ChIPseqR 1.64.0
Identifying Protein Binding Sites in High-Throughput Sequencing Data
7 versions - Latest release: 4 months ago - 49 thousand downloads total - 1 maintainer
Top 2.5% on bioconductor.org
mzR 2.44.0
parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
6 versions - Latest release: 3 months ago - 23 dependent packages - 1.16 million downloads total - 42 stars on GitHub - 1 maintainer
Related Keywords
Software 268 DataImport 95 DataRepresentation 66 Sequencing 43 Visualization 30 MassSpectrometry 27 Proteomics 27 bioconductor 26 Metabolomics 25 ImmunoOncology 25 SingleCell 23 GeneExpression 19 r 19 Annotation 18 Genetics 18 QualityControl 17 Clustering 16 Transcriptomics 15 DifferentialExpression 13 mass-spectrometry 13 Coverage 13 RNASeq 13 bioconductor-package 12 ThirdPartyClient 11 GenomeAnnotation 11 CellBasedAssays 10 GUI 10 bioinformatics 10 Microarray 9 u24ca289073 9 Normalization 8 Spatial 8 proteomics 8 Alignment 8 metabolomics 7 ReportWriting 7 BiomedicalInformatics 7 SequenceMatching 7 Preprocessing 7 Transcription 6 AssayDomain 6 rstats 6 WorkflowStep 6 core-package 6 KEGG 5 GO 5 DimensionReduction 5 Classification 5 FlowCytometry 5 genomics 5 MicrotitrePlateAssay 5 tidyverse 5 Network 4 SNP 4 StatisticalMethod 4 ExperimentalDesign 4 ShinyApps 4 Cheminformatics 4 Pharmacogenetics 4 Pharmacogenomics 4 Pathways 4 GenomeAssembly 4 hdf5 4 package 3 HiC 3 iseeu 3 hacktoberfest 3 ChIPSeq 3 GeneSetEnrichment 3 Microbiome 3 rna 3 MultipleComparison 3 OneChannel 3 BiologicalQuestion 3 transcriptomics 3 rpackage 3 GraphAndNetwork 3 gds-format 3 PrincipalComponent 2 TwoChannel 2 tibble 2 singlecellexperiment 2 pca 2 snp 2 MicrobiomeData 2 Technology 2 ProprietaryPlatforms 2 human-cell-atlas 2 sequences 2 Bioinformatics 2 multiplatform 2 GenotypingArray 2 infrastructure 2 Metagenomics 2 fast 2 HighThroughputSequencing 2 ImagingMassSpectrometry 2 ontology 1 annotation 1 microscopy 1