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bioconductor.org "DataImport" keyword

View the packages on the bioconductor.org package registry that are tagged with the "DataImport" keyword.

Top 0.9% on bioconductor.org
VariantAnnotation 1.54.1
Annotation of Genetic Variants
7 versions - Latest release: 4 months ago - 93 dependent packages - 1.87 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.66.0
FASTQ input and manipulation
6 versions - Latest release: 5 months ago - 36 dependent packages - 1.82 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
MSnbase 2.34.1
Base Functions and Classes for Mass Spectrometry and Proteomics
7 versions - Latest release: 4 months ago - 30 dependent packages - 495 thousand downloads total - 123 stars on GitHub - 1 maintainer
rmspc 1.14.0
Multiple Sample Peak Calling
5 versions - Latest release: 4 months ago - 6.32 thousand downloads total - 20 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
SingleCellExperiment 1.30.1
S4 Classes for Single Cell Data
7 versions - Latest release: 4 months ago - 201 dependent packages - 1.64 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
ggtree 3.16.3
an R package for visualization of tree and annotation data
8 versions - Latest release: about 2 months ago - 28 dependent packages - 1.8 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
HDF5Array 1.36.0
HDF5 datasets as array-like objects in R
7 versions - Latest release: 5 months ago - 54 dependent packages - 1.45 million downloads total - 1 maintainer
Top 3.2% on bioconductor.org
oligo 1.72.0
Preprocessing tools for oligonucleotide arrays
7 versions - Latest release: 4 months ago - 11 dependent packages - 451 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.76.0
Efficient manipulation of biological strings
10 versions - Latest release: 5 months ago - 333 dependent packages - 8.21 million downloads total - 1 maintainer
scCB2 1.18.0
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
5 versions - Latest release: 4 months ago - 8 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.54.1
Analyze Illumina Infinium DNA methylation arrays
7 versions - Latest release: 4 months ago - 31 dependent packages - 868 thousand downloads total - 61 stars on GitHub - 1 maintainer
Top 0.4% on bioconductor.org
rtracklayer 1.68.0
R interface to genome annotation files and the UCSC genome browser
5 versions - Latest release: 5 months ago - 251 dependent packages - 4.64 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.52.1
R Interface to HDF5
9 versions - Latest release: 3 months ago - 69 dependent packages - 2.8 million downloads total - 67 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.76.0
Get data from NCBI Gene Expression Omnibus (GEO)
5 versions - Latest release: 5 months ago - 47 dependent packages - 2.14 million downloads total - 98 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.36.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
8 versions - Latest release: 5 months ago - 96 dependent packages - 859 thousand downloads total - 1 maintainer
MuData 1.12.0
Serialization for MultiAssayExperiment Objects
5 versions - Latest release: 4 months ago - 6.57 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
GenomicAlignments 1.44.0
Representation and manipulation of short genomic alignments
7 versions - Latest release: 5 months ago - 132 dependent packages - 4.4 million downloads total - 1 maintainer
ORFik 1.28.2
Open Reading Frames in Genomics
10 versions - Latest release: 4 months ago - 2 dependent packages - 23.9 thousand downloads total - 34 stars on GitHub - 1 maintainer
faers 1.4.0
R interface for FDA Adverse Event Reporting System
4 versions - Latest release: 4 months ago - 4.6 thousand downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.64.3
Linear Models for Microarray and Omics Data
15 versions - Latest release: about 1 month ago - 322 dependent packages - 6.25 million downloads total - 1 maintainer
SurfR 1.4.1
Surface Protein Prediction and Identification
8 versions - Latest release: 2 months ago - 0 stars on GitHub - 1 maintainer
svaRetro 1.14.0
Retrotransposed transcript detection from structural variants
5 versions - Latest release: 4 months ago - 1 stars on GitHub - 1 maintainer
alabaster 1.8.0
Umbrella for the Alabaster Framework
5 versions - Latest release: 4 months ago - 5.21 thousand downloads total - 1 maintainer
autonomics 1.16.0
Unified Statistical Modeling of Omics Data
8 versions - Latest release: 4 months ago - 8 thousand downloads total - 3 stars on GitHub - 1 maintainer
Structstrings 1.24.0
Implementation of the dot bracket annotations with Biostrings
6 versions - Latest release: 4 months ago - 3 dependent packages - 14.8 thousand downloads total - 5 stars on GitHub - 1 maintainer
alabaster.bumpy 1.8.1
Save and Load BumpyMatrices to/from file
6 versions - Latest release: 2 months ago - 1 dependent package - 5.91 thousand downloads total - 1 maintainer
gemma.R 3.4.5
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...
16 versions - Latest release: about 2 months ago - 6.94 thousand downloads total - 10 stars on GitHub - 1 maintainer
cellmigRation 1.16.0
Track Cells, Analyze Cell Trajectories and Compute Migration Statistics
5 versions - Latest release: 5 months ago - 6.98 thousand downloads total - 0 stars on GitHub - 1 maintainer
ggkegg 1.6.0
Analyzing and visualizing KEGG information using the grammar of graphics
14 versions - Latest release: 4 months ago - 15.7 thousand downloads total - 232 stars on GitHub - 1 maintainer
rfaRm 1.20.0
An R interface to the Rfam database
7 versions - Latest release: 4 months ago - 8.6 thousand downloads total - 2 maintainers
Top 3.0% on bioconductor.org
ChemmineOB 1.46.0
R interface to a subset of OpenBabel functionalities
5 versions - Latest release: 5 months ago - 2 dependent packages - 232 thousand downloads total - 10 stars on GitHub - 1 maintainer
MsBackendMetaboLights 1.2.0
Retrieve Mass Spectrometry Data from MetaboLights
2 versions - Latest release: 4 months ago - 2.16 thousand downloads total - 2 stars on GitHub - 1 maintainer
CTdata 1.8.0
Data companion to CTexploreR
5 versions - Latest release: 4 months ago - 1 dependent package - 4.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.0% on bioconductor.org
monocle 2.36.0
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
6 versions - Latest release: 4 months ago - 6 dependent packages - 398 thousand downloads total - 1 maintainer
Top 5.9% on bioconductor.org
systemPipeR 2.14.2
systemPipeR: Workflow Environment for Data Analysis and Report Generation
6 versions - Latest release: 2 months ago - 3 dependent packages - 241 thousand downloads total - 54 stars on GitHub - 1 maintainer
RGMQL 1.28.0
GenoMetric Query Language for R/Bioconductor
6 versions - Latest release: 4 months ago - 8.43 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
mia 1.16.1
Microbiome analysis
6 versions - Latest release: about 2 months ago - 7 dependent packages - 125 thousand downloads total - 53 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
rpx 2.16.0
R Interface to the ProteomeXchange Repository
6 versions - Latest release: 5 months ago - 3 dependent packages - 61 thousand downloads total - 5 stars on GitHub - 1 maintainer
NeuCA 1.14.0
NEUral network-based single-Cell Annotation tool
7 versions - Latest release: 3 months ago - 3.92 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
bamsignals 1.40.0
Extract read count signals from bam files
5 versions - Latest release: 5 months ago - 7 dependent packages - 119 thousand downloads total - 15 stars on GitHub - 1 maintainer
Top 8.3% on bioconductor.org
MANOR 1.80.0
CGH Micro-Array NORmalization
5 versions - Latest release: 4 months ago - 37.5 thousand downloads total - 1 maintainer
CoSIA 1.8.0
An Investigation Across Different Species and Tissues
6 versions - Latest release: 4 months ago - 3.68 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
ExperimentHub 2.16.1
Client to access ExperimentHub resources
6 versions - Latest release: about 1 month ago - 61 dependent packages - 616 thousand downloads total - 10 stars on GitHub - 1 maintainer
iSEEtree 1.2.0
Interactive visualisation for microbiome data
2 versions - Latest release: 5 months ago - 3.01 thousand downloads total - 3 stars on GitHub - 1 maintainer
MsBackendSql 1.8.0
SQL-based Mass Spectrometry Data Backend
5 versions - Latest release: 4 months ago - 5.46 thousand downloads total - 4 stars on GitHub - 1 maintainer
RImmPort 1.36.0
RImmPort: Enabling Ready-for-analysis Immunology Research Data
5 versions - Latest release: 4 months ago - 13.8 thousand downloads total - 2 maintainers
SpatialExperimentIO 1.0.0
Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object
1 version - Latest release: 5 months ago - 1.86 thousand downloads total - 16 stars on GitHub - 1 maintainer
assorthead 1.2.0
Assorted Header-Only C++ Libraries
3 versions - Latest release: 5 months ago - 180 thousand downloads total - 0 stars on GitHub - 1 maintainer
transomics2cytoscape 1.18.0
A tool set for 3D Trans-Omic network visualization with Cytoscape
6 versions - Latest release: 4 months ago - 8.35 thousand downloads total - 1 maintainer
MGnifyR 1.4.0
R interface to EBI MGnify metagenomics resource
3 versions - Latest release: 5 months ago - 4.43 thousand downloads total - 22 stars on GitHub - 1 maintainer
mitoClone2 1.14.0
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Muta...
6 versions - Latest release: 4 months ago - 6.96 thousand downloads total - 1 stars on GitHub - 1 maintainer
BayesSpace 1.18.4
Clustering and Resolution Enhancement of Spatial Transcriptomes
8 versions - Latest release: 8 days ago - 1 dependent package - 23.2 thousand downloads total - 150 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
CNEr 1.43.0
CNE Detection and Visualization
5 versions - Latest release: 4 months ago - 1 dependent package - 290 thousand downloads total - 4 stars on GitHub - 1 maintainer
recount3 1.18.0
Explore and download data from the recount3 project
5 versions - Latest release: 4 months ago - 24.1 thousand downloads total - 36 stars on GitHub - 1 maintainer
Top 8.7% on bioconductor.org
biobroom 1.40.0
Turn Bioconductor objects into tidy data frames
5 versions - Latest release: 4 months ago - 1 dependent package - 36.2 thousand downloads total - 50 stars on GitHub - 1 maintainer
SPIAT 1.10.0
Spatial Image Analysis of Tissues
9 versions - Latest release: 5 months ago - 9.01 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 3.0% on bioconductor.org
cytolib 2.20.0
C++ infrastructure for representing and interacting with the gated cytometry data
8 versions - Latest release: 4 months ago - 3 dependent packages - 277 thousand downloads total - 1 maintainer
Top 2.5% on bioconductor.org
mzR 2.42.0
parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
5 versions - Latest release: 4 months ago - 23 dependent packages - 1.04 million downloads total - 42 stars on GitHub - 1 maintainer
Top 7.6% on bioconductor.org
biomformat 1.36.0
An interface package for the BIOM file format
5 versions - Latest release: 4 months ago - 8 dependent packages - 629 thousand downloads total - 7 stars on GitHub - 1 maintainer
CTexploreR 1.4.0
Explores Cancer Testis Genes
3 versions - Latest release: 4 months ago - 3.75 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.1% on bioconductor.org
codelink 1.76.0
Manipulation of Codelink microarray data
5 versions - Latest release: 4 months ago - 1 dependent package - 40.7 thousand downloads total - 0 stars on GitHub - 2 maintainers
ReUseData 1.8.0
Reusable and reproducible Data Management
7 versions - Latest release: 4 months ago - 4.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
PepsNMR 1.26.0
Pre-process 1H-NMR FID signals
5 versions - Latest release: 4 months ago - 1 dependent package - 16.1 thousand downloads total - 9 stars on GitHub - 1 maintainer
LOBSTAHS 1.34.1
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
6 versions - Latest release: 8 days ago - 15.1 thousand downloads total - 3 maintainers
Top 6.7% on bioconductor.org
segmentSeq 2.42.0
Methods for identifying small RNA loci from high-throughput sequencing data
5 versions - Latest release: 4 months ago - 40.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
AlpsNMR 4.10.0
Automated spectraL Processing System for NMR
5 versions - Latest release: 4 months ago - 11.4 thousand downloads total - 16 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
ReadqPCR 1.54.0
Read qPCR data
5 versions - Latest release: 4 months ago - 1 dependent package - 65.7 thousand downloads total - 1 maintainer
UCSC.utils 1.4.0
Low-level utilities to retrieve data from the UCSC Genome Browser
3 versions - Latest release: 4 months ago - 2 dependent packages - 1.06 million downloads total - 1 maintainer
Top 5.6% on bioconductor.org
HTqPCR 1.62.0
Automated analysis of high-throughput qPCR data
5 versions - Latest release: 4 months ago - 2 dependent packages - 57.3 thousand downloads total - 1 maintainer
schex 1.22.0
Hexbin plots for single cell omics data
6 versions - Latest release: 4 months ago - 3 dependent packages - 19.8 thousand downloads total - 74 stars on GitHub - 1 maintainer
sevenbridges 1.38.0
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
5 versions - Latest release: 5 months ago - 19.3 thousand downloads total - 35 stars on GitHub - 1 maintainer
chihaya 1.8.0
Save Delayed Operations to a HDF5 File
5 versions - Latest release: 4 months ago - 1 dependent package - 7.13 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.1% on bioconductor.org
Rhtslib 3.4.0
HTSlib high-throughput sequencing library as an R package
6 versions - Latest release: 5 months ago - 5 dependent packages - 3.16 million downloads total - 1 maintainer
cogena 1.42.0
co-expressed gene-set enrichment analysis
5 versions - Latest release: 4 months ago - 23.4 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 6.4% on bioconductor.org
hpar 1.50.0
Human Protein Atlas in R
5 versions - Latest release: 4 months ago - 3 dependent packages - 62.1 thousand downloads total - 1 maintainer
Streamer 1.54.0
Enabling stream processing of large files
5 versions - Latest release: 4 months ago - 28.4 thousand downloads total - 1 maintainer
Top 9.4% on bioconductor.org
R453Plus1Toolbox 1.58.0
A package for importing and analyzing data from Roche's Genome Sequencer System
5 versions - Latest release: 4 months ago - 32.5 thousand downloads total - 1 maintainer
SRAdb 1.70.0
A compilation of metadata from NCBI SRA and tools
6 versions - Latest release: 4 months ago - 123 thousand downloads total - 1 stars on GitHub - 1 maintainer
LoomExperiment 1.26.1
LoomExperiment container
6 versions - Latest release: 3 months ago - 2 dependent packages - 43.3 thousand downloads total - 1 maintainer
Doscheda 1.30.0
A DownStream Chemo-Proteomics Analysis Pipeline
5 versions - Latest release: 4 months ago - 13.5 thousand downloads total - 1 maintainer
alabaster.files 1.6.0
Wrappers to Save Common File Formats
4 versions - Latest release: 4 months ago - 4.33 thousand downloads total - 1 maintainer
alabaster.mae 1.8.0
Load and Save MultiAssayExperiments
5 versions - Latest release: 4 months ago - 1 dependent package - 6.62 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
dittoSeq 1.20.0
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
7 versions - Latest release: 4 months ago - 6 dependent packages - 83.8 thousand downloads total - 1 maintainer
ChIPComp 1.38.0
Quantitative comparison of multiple ChIP-seq datasets
5 versions - Latest release: 4 months ago - 21 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
mzID 1.46.0
An mzIdentML parser for R
5 versions - Latest release: 4 months ago - 5 dependent packages - 336 thousand downloads total - 1 maintainer
NanoStringNCTools 1.16.1
NanoString nCounter Tools
7 versions - Latest release: about 1 month ago - 2 dependent packages - 24.2 thousand downloads total - 1 maintainer
QSutils 1.26.0
Quasispecies Diversity
5 versions - Latest release: 4 months ago - 25.7 thousand downloads total - 1 maintainer
DegNorm 1.18.0
DegNorm: degradation normalization for RNA-seq data
5 versions - Latest release: 4 months ago - 8.89 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
GenomicFiles 1.44.1
Distributed computing by file or by range
6 versions - Latest release: 4 months ago - 12 dependent packages - 180 thousand downloads total - 1 maintainer
GEOfastq 1.16.0
Downloads ENA Fastqs With GEO Accessions
5 versions - Latest release: 4 months ago - 8.15 thousand downloads total - 4 stars on GitHub - 1 maintainer
cbpManager 1.16.0
Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Canc...
5 versions - Latest release: 4 months ago - 8.26 thousand downloads total - 9 stars on GitHub - 1 maintainer
brendaDb 1.22.0
The BRENDA Enzyme Database
5 versions - Latest release: 5 months ago - 9.69 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
puma 3.50.0
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and ex...
5 versions - Latest release: 4 months ago - 1 dependent package - 53.1 thousand downloads total - 1 maintainer
ENmix 1.44.3
Quality control and analysis tools for Illumina DNA methylation BeadChip
9 versions - Latest release: about 1 month ago - 39.3 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
illuminaio 0.50.0
Parsing Illumina Microarray Output Files
5 versions - Latest release: 4 months ago - 12 dependent packages - 482 thousand downloads total - 5 stars on GitHub - 1 maintainer
SynExtend 1.20.2
Tools for Working With Synteny Objects
6 versions - Latest release: 3 months ago - 9.11 thousand downloads total - 1 stars on GitHub - 1 maintainer
MoleculeExperiment 1.8.0
Prioritising a molecule-level storage of Spatial Transcriptomics Data
8 versions - Latest release: 5 months ago - 5.83 thousand downloads total - 12 stars on GitHub - 1 maintainer
txdbmaker 1.4.2
Tools for making TxDb objects from genomic annotations
7 versions - Latest release: 2 months ago - 8 dependent packages - 108 thousand downloads total - 1 maintainer
bedbaser 1.0.3
A BEDbase client
2 versions - Latest release: about 2 months ago - 1.47 thousand downloads total - 1 stars on GitHub - 1 maintainer
biscuiteer 1.22.0
Convenience Functions for Biscuit
5 versions - Latest release: 4 months ago - 12.8 thousand downloads total - 6 stars on GitHub - 1 maintainer
Related Keywords
Software 353 Sequencing 114 Infrastructure 93 GeneExpression 75 DataRepresentation 75 ImmunoOncology 73 Visualization 66 QualityControl 66 Preprocessing 66 RNASeq 59 SingleCell 57 Coverage 46 Alignment 42 Transcriptomics 41 DifferentialExpression 37 Clustering 37 Genetics 36 Proteomics 36 Microarray 36 Normalization 35 bioconductor 33 Transcription 29 Annotation 28 r 27 MassSpectrometry 26 MultipleComparison 25 Metabolomics 22 TwoChannel 21 ThirdPartyClient 21 SequenceMatching 20 OneChannel 19 BiomedicalInformatics 19 ChIPSeq 18 bioinformatics 17 FunctionalGenomics 17 BatchEffect 17 Epigenetics 16 DNAMethylation 16 Regression 15 GeneSetEnrichment 15 Bayesian 15 GUI 14 SNP 14 Spatial 14 Classification 13 Pathways 13 bioconductor-package 12 SystemsBiology 12 FlowCytometry 12 GenomeAnnotation 12 ProprietaryPlatforms 11 TimeCourse 11 CellBasedAssays 11 GeneRegulation 11 Network 11 Cheminformatics 10 WorkflowStep 10 CellBiology 10 Microbiome 10 CopyNumberVariation 10 DifferentialMethylation 10 VariantAnnotation 9 rstats 9 AlternativeSplicing 9 MethylationArray 9 GO 9 mRNAMicroarray 9 GraphAndNetwork 8 MicrotitrePlateAssay 8 MethylSeq 8 DimensionReduction 8 ExperimentalDesign 8 DNASeq 7 StatisticalMethod 7 KEGG 7 DifferentialSplicing 7 MultipleSequenceAlignment 7 HiC 7 genomics 7 ReportWriting 7 WholeGenome 7 r-package 6 ChipOnChip 6 ATACSeq 5 PrincipalComponent 5 CpGIsland 5 rna-seq 5 GeneticVariability 5 Pharmacogenomics 5 ExonArray 5 u24ca289073 5 ShinyApps 5 DNA3DStructure 4 Pharmacogenetics 4 ExperimentHubSoftware 4 PeakDetection 4 GenomeAssembly 4 BiologicalQuestion 4 shiny 4 Metagenomics 4