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

bioconductor.org "Infrastructure" keyword

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 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 - 4.29 million downloads total - 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 - 2.79 million downloads total - 1 maintainer
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 - 8.76 million downloads total - 63 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 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 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: 3 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 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 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 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 - 7.71 million 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
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 - 1.73 million downloads total - 1 maintainer
TnT 1.32.0
Interactive Visualization for Genomic Features
7 versions - Latest release: 3 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
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
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
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 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
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: 3 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 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 0.2% on bioconductor.org
Biostrings 2.78.0
Efficient manipulation of biological strings
11 versions - Latest release: 4 months ago - 333 dependent packages - 9.39 million downloads total - 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
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 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
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
biodbNcbi 1.13.0
biodbNcbi, a library for connecting to NCBI Databases.
6 versions - Latest release: 4 months ago - 6.88 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
BiocCheck 1.46.3
Bioconductor-specific package checks
10 versions - Latest release: about 1 month ago - 6 dependent packages - 301 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 3.0% on bioconductor.org
ChemmineOB 1.48.0
R interface to a subset of OpenBabel functionalities
6 versions - Latest release: 3 months ago - 2 dependent packages - 241 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 7.4% on bioconductor.org
panp 1.80.0
Presence-Absence Calls from Negative Strand Matching Probesets
6 versions - Latest release: 3 months ago - 42.2 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
AnnotationHub 4.0.0
Client to access AnnotationHub resources
8 versions - Latest release: 3 months ago - 97 dependent packages - 1.52 million downloads total - 13 stars on GitHub - 1 maintainer
biodb 1.18.0
Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases
7 versions - Latest release: 3 months ago - 10 dependent packages - 18.1 thousand downloads total - 11 stars on GitHub - 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 - 9.3 million downloads total - 1 maintainer
biodbUniprot 1.15.0
biodbUniprot, a library for connecting to the Uniprot Database
6 versions - Latest release: 3 months ago - 7.11 thousand downloads total - 2 stars on GitHub - 1 maintainer
gDRstyle 1.8.0
A package with style requirements for the gDR suite
6 versions - Latest release: 3 months ago - 4 dependent packages - 6.71 thousand downloads total - 3 stars on GitHub - 1 maintainer
Structstrings 1.26.0
Implementation of the dot bracket annotations with Biostrings
7 versions - Latest release: 4 months ago - 3 dependent packages - 17.4 thousand downloads total - 5 stars on GitHub - 1 maintainer
MsBackendMetaboLights 1.4.2
Retrieve Mass Spectrometry Data from MetaboLights
3 versions - Latest release: 4 months ago - 4.19 thousand downloads total - 2 stars on GitHub - 1 maintainer
QFeatures 1.20.0
Quantitative features for mass spectrometry data
8 versions - Latest release: 3 months ago - 6 dependent packages - 152 thousand downloads total - 27 stars on GitHub - 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 - 440 thousand downloads total - 1 maintainer
HiCBricks 1.28.0
Framework for Storing and Accessing Hi-C Data Through HDF Files
6 versions - Latest release: 3 months ago - 1 dependent package - 16.7 thousand downloads total - 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
AnVIL 1.22.5
Bioconductor on the AnVIL compute environment
18 versions - Latest release: 1 day ago - 4 dependent packages - 59.4 thousand downloads total - 1 maintainer
Top 5.7% on bioconductor.org
GenVisR 1.42.2
Genomic Visualizations in R
7 versions - Latest release: about 1 month ago - 64.6 thousand downloads total - 194 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
sparseMatrixStats 1.22.0
Summary Statistics for Rows and Columns of Sparse Matrices
6 versions - Latest release: 4 months ago - 11 dependent packages - 1.61 million downloads total - 54 stars on GitHub - 1 maintainer
gDRutils 1.8.0
A package with helper functions for processing drug response data
6 versions - Latest release: 3 months ago - 3 dependent packages - 7.29 thousand downloads total - 0 stars on GitHub - 1 maintainer
TileDBArray 1.20.0
Using TileDB as a DelayedArray Backend
7 versions - Latest release: 4 months ago - 10.6 thousand downloads total - 10 stars on GitHub - 1 maintainer
epivizr 2.40.0
R Interface to epiviz web app
6 versions - Latest release: 3 months ago - 2 dependent packages - 35.9 thousand 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 - 2.02 million downloads total - 1 maintainer
Top 4.5% on bioconductor.org
convert 1.86.0
Convert Microarray Data Objects
6 versions - Latest release: 3 months ago - 4 dependent packages - 80.8 thousand downloads total - 1 maintainer
Top 3.9% on bioconductor.org
preprocessCore 1.72.0
A collection of pre-processing functions
6 versions - Latest release: 3 months ago - 51 dependent packages - 2.85 million downloads total - 20 stars on GitHub - 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
ReUseData 1.10.0
Reusable and reproducible Data Management
8 versions - Latest release: 3 months ago - 5.94 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
Icens 1.82.0
NPMLE for Censored and Truncated Data
6 versions - Latest release: 3 months ago - 1 dependent package - 145 thousand downloads total - 1 maintainer
Top 3.6% on bioconductor.org
SeqArray 1.50.1
Data management of large-scale whole-genome sequence variant calls using GDS files
19 versions - Latest release: about 1 month ago - 11 dependent packages - 146 thousand downloads total - 46 stars on GitHub - 1 maintainer
Top 6.3% on bioconductor.org
ChemmineR 3.62.0
Cheminformatics Toolkit for R
6 versions - Latest release: 3 months ago - 8 dependent packages - 530 thousand downloads total - 16 stars on GitHub - 1 maintainer
cummeRbund 2.51.0
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
6 versions - Latest release: 3 months ago - 594 thousand downloads total - 1 maintainer
Top 6.0% on bioconductor.org
widgetTools 1.88.0
Creates an interactive tcltk widget
6 versions - Latest release: 3 months ago - 3 dependent packages - 281 thousand downloads total - 1 maintainer
SQLDataFrame 1.23.0
Representation of SQL tables in DataFrame metaphor
7 versions - Latest release: 3 months ago - 10 thousand downloads total - 2 stars on GitHub - 1 maintainer
doseR 1.26.0
doseR
6 versions - Latest release: 3 months ago - 12.5 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
plyranges 1.30.1
A fluent interface for manipulating GenomicRanges
6 versions - Latest release: 4 months ago - 22 dependent packages - 151 thousand downloads total - 127 stars on GitHub - 1 maintainer
mimager 1.34.0
mimager: The Microarray Imager
6 versions - Latest release: 4 months ago - 16.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
Modstrings 1.26.0
Working with modified nucleotide sequences
6 versions - Latest release: 3 months ago - 4 dependent packages - 20.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
BiocFHIR 1.12.0
Illustration of FHIR ingestion and transformation using R
6 versions - Latest release: 3 months ago - 7.07 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 7.5% on bioconductor.org
webbioc 1.82.0
Bioconductor Web Interface
6 versions - Latest release: 3 months ago - 42 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
biovizBase 1.58.0
Basic graphic utilities for visualization of genomic data.
6 versions - Latest release: 3 months ago - 17 dependent packages - 1.34 million downloads total - 1 maintainer
Top 8.2% on bioconductor.org
ChIPsim 1.64.0
Simulation of ChIP-seq experiments
6 versions - Latest release: 3 months ago - 47.3 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
genomeIntervals 1.66.0
Operations on genomic intervals
6 versions - Latest release: 3 months ago - 3 dependent packages - 94.2 thousand downloads total - 1 maintainer
MoleculeExperiment 1.10.0
Prioritising a molecule-level storage of Spatial Transcriptomics Data
9 versions - Latest release: 3 months ago - 7.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
DeeDeeExperiment 1.0.0
DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results
1 version - Latest release: 4 months ago - 1.09 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.1% on bioconductor.org
pdInfoBuilder 1.74.0
Platform Design Information Package Builder
6 versions - Latest release: 4 months ago - 61.4 thousand downloads total - 1 maintainer
ExperimentHubData 1.36.0
Add resources to ExperimentHub
6 versions - Latest release: 3 months ago - 3 dependent packages - 46.6 thousand downloads total - 1 maintainer
MsBackendMassbank 1.18.2
Mass Spectrometry Data Backend for MassBank record Files
9 versions - Latest release: about 1 month ago - 27.4 thousand downloads total - 3 stars on GitHub - 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 - 9.44 million downloads total - 1 maintainer
Top 7.0% on bioconductor.org
Rhdf5lib 1.32.0
hdf5 library as an R package
8 versions - Latest release: 4 months ago - 3 dependent packages - 3.12 million downloads total - 6 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
basilisk 1.22.0
Freezing Python Dependencies Inside Bioconductor Packages
8 versions - Latest release: 4 months ago - 27 dependent packages - 301 thousand downloads total - 24 stars on GitHub - 1 maintainer
arrayMvout 1.68.0
multivariate outlier detection for expression array QA
6 versions - Latest release: 4 months ago - 45.4 thousand downloads total - 1 maintainer
ontoProc 2.4.0
processing of ontologies of anatomy, cell lines, and so on
8 versions - Latest release: 4 months ago - 3 dependent packages - 25.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
MsFeatures 1.18.0
Functionality for Mass Spectrometry Features
6 versions - Latest release: 4 months ago - 2 dependent packages - 143 thousand downloads total - 7 stars on GitHub - 1 maintainer
MetaboAnnotation 1.14.0
Utilities for Annotation of Metabolomics Data
9 versions - Latest release: 4 months ago - 20.1 thousand downloads total - 17 stars on GitHub - 1 maintainer
biocmake 1.2.0
CMake for Bioconductor
3 versions - Latest release: 4 months ago - 13.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
Related Keywords
Software 268 DataImport 95 DataRepresentation 66 Sequencing 43 Visualization 30 MassSpectrometry 27 Proteomics 27 bioconductor 26 ImmunoOncology 25 Metabolomics 25 SingleCell 23 GeneExpression 19 r 19 Annotation 18 Genetics 18 QualityControl 17 Clustering 16 Transcriptomics 15 mass-spectrometry 13 RNASeq 13 Coverage 13 DifferentialExpression 13 bioconductor-package 12 GenomeAnnotation 11 ThirdPartyClient 11 bioinformatics 10 GUI 10 CellBasedAssays 10 Microarray 9 u24ca289073 9 proteomics 8 Alignment 8 Spatial 8 Normalization 8 metabolomics 7 BiomedicalInformatics 7 SequenceMatching 7 ReportWriting 7 Preprocessing 7 rstats 6 Transcription 6 WorkflowStep 6 core-package 6 AssayDomain 6 genomics 5 FlowCytometry 5 DimensionReduction 5 KEGG 5 GO 5 Classification 5 tidyverse 5 MicrotitrePlateAssay 5 GenomeAssembly 4 Network 4 hdf5 4 Pharmacogenomics 4 ShinyApps 4 Pharmacogenetics 4 Cheminformatics 4 StatisticalMethod 4 SNP 4 ExperimentalDesign 4 Pathways 4 rna 3 rpackage 3 BiologicalQuestion 3 ChIPSeq 3 transcriptomics 3 MultipleComparison 3 OneChannel 3 package 3 GeneSetEnrichment 3 iseeu 3 gds-format 3 GraphAndNetwork 3 hacktoberfest 3 Microbiome 3 HiC 3 Bioinformatics 2 HighThroughputSequencing 2 MicrobiomeData 2 sequences 2 Metagenomics 2 infrastructure 2 ImagingMassSpectrometry 2 multiplatform 2 fast 2 GenotypingArray 2 singlecellexperiment 2 human-cell-atlas 2 ProprietaryPlatforms 2 tibble 2 snp 2 Technology 2 pca 2 PrincipalComponent 2 TwoChannel 2 dimensionality-reduction 1 dplyr 1 ggplot2 1