Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "DataRepresentation" keyword
Top 0.2% on bioconductor.org
10 versions - Latest release: 20 days ago - 342 dependent packages - 7.22 million downloads total - 1 maintainer
GenomeInfoDb 1.40.0
Utilities for manipulating chromosome names, including modifying them to follow a particular nami...10 versions - Latest release: 20 days ago - 342 dependent packages - 7.22 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
4 versions - Latest release: 20 days ago - 96 dependent packages - 622 thousand downloads total - 1 maintainer
scater 1.32.0
Single-Cell Analysis Toolkit for Gene Expression Data in R4 versions - Latest release: 20 days ago - 96 dependent packages - 622 thousand downloads total - 1 maintainer
Top 0.2% on bioconductor.org
6 versions - Latest release: 20 days ago - 333 dependent packages - 6.29 million downloads total - 1 maintainer
Biostrings 2.72.0
Efficient manipulation of biological strings6 versions - Latest release: 20 days ago - 333 dependent packages - 6.29 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
5 versions - Latest release: 20 days ago - 740 dependent packages - 7.45 million downloads total - 1 maintainer
S4Vectors 0.42.0
Foundation of vector-like and list-like containers in Bioconductor5 versions - Latest release: 20 days ago - 740 dependent packages - 7.45 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
4 versions - Latest release: 20 days ago - 604 dependent packages - 6.34 million downloads total - 1 maintainer
GenomicRanges 1.56.0
Representation and manipulation of genomic intervals4 versions - Latest release: 20 days ago - 604 dependent packages - 6.34 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
3 versions - Latest release: 20 days ago - 563 dependent packages - 8.04 million downloads total - 1 maintainer
IRanges 2.38.0
Foundation of integer range manipulation in Bioconductor3 versions - Latest release: 20 days ago - 563 dependent packages - 8.04 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
4 versions - Latest release: 20 days ago - 54 dependent packages - 990 thousand downloads total - 1 maintainer
HDF5Array 1.32.0
HDF5 backend for DelayedArray objects4 versions - Latest release: 20 days ago - 54 dependent packages - 990 thousand downloads total - 1 maintainer
Top 0.5% on bioconductor.org
4 versions - Latest release: 9 days ago - 111 dependent packages - 5 million downloads total - 1 maintainer
DelayedArray 0.30.1
A unified framework for working transparently with on-disk and in-memory array-like datasets4 versions - Latest release: 9 days ago - 111 dependent packages - 5 million downloads total - 1 maintainer
Top 0.8% on bioconductor.org
5 versions - Latest release: 20 days ago - 129 dependent packages - 2 million downloads total - 1 maintainer
BSgenome 1.72.0
Software infrastructure for efficient representation of full genomes and their SNPs5 versions - Latest release: 20 days ago - 129 dependent packages - 2 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
3 versions - Latest release: 20 days ago - 36 dependent packages - 6.03 million downloads total - 1 maintainer
XVector 0.44.0
Foundation of external vector representation and manipulation in Bioconductor3 versions - Latest release: 20 days ago - 36 dependent packages - 6.03 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
3 versions - Latest release: 20 days ago - 201 dependent packages - 1.07 million downloads total - 1 maintainer
SingleCellExperiment 1.26.0
S4 Classes for Single Cell Data3 versions - Latest release: 20 days ago - 201 dependent packages - 1.07 million downloads total - 1 maintainer
chihaya 1.2.0
Save Delayed Operations to a HDF5 File3 versions - Latest release: 6 months ago - 1 dependent package - 1.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
4 versions - Latest release: 15 days ago - 15 dependent packages - 928 thousand downloads total - 4 stars on GitHub - 1 maintainer
beachmat 2.20.0
Compiling Bioconductor to Handle Each Matrix Type4 versions - Latest release: 15 days ago - 15 dependent packages - 928 thousand downloads total - 4 stars on GitHub - 1 maintainer
matter 2.6.1
Scientific computing for out-of-memory signals and images5 versions - Latest release: 11 days ago - 2 dependent packages - 19 thousand downloads total - 52 stars on GitHub - 1 maintainer
VariantExperiment 1.18.0
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend4 versions - Latest release: 22 days ago - 5.08 thousand downloads total - 1 stars on GitHub - 1 maintainer
GDSArray 1.24.0
Representing GDS files as array-like objects3 versions - Latest release: 22 days ago - 3 dependent packages - 10.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
3 versions - Latest release: 22 days ago - 9 dependent packages - 226 thousand downloads total - 421 stars on GitHub - 1 maintainer
maftools 2.20.0 💰
Summarize, Analyze and Visualize MAF Files3 versions - Latest release: 22 days ago - 9 dependent packages - 226 thousand downloads total - 421 stars on GitHub - 1 maintainer
OmnipathR 3.10.1
OmniPath web service client and more3 versions - Latest release: 6 months ago - 3 dependent packages - 23.4 thousand downloads total - 1 maintainer
plethy 1.40.0 removed
R framework for exploration and analysis of respirometry data2 versions - Latest release: 6 months ago - 16.1 thousand downloads total - 1 maintainer
VennDetail 1.18.0
A package for visualization and extract details3 versions - Latest release: 6 months ago - 12 thousand downloads total - 24 stars on GitHub - 1 maintainer
Ularcirc 1.20.0
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)3 versions - Latest release: 6 months ago - 6.51 thousand downloads total - 1 maintainer
rexposome 1.24.1
Exposome exploration and outcome data analysis3 versions - Latest release: 6 months ago - 1 dependent package - 10.3 thousand downloads total - 1 maintainer
OSAT 1.50.0
OSAT: Optimal Sample Assignment Tool3 versions - Latest release: 6 months ago - 21.7 thousand downloads total - 1 maintainer
OMICsPCA 1.20.0
An R package for quantitative integration and analysis of multiple omics assays from heterogeneou...3 versions - Latest release: 6 months ago - 7.29 thousand downloads total - 1 maintainer
QTLExperiment 1.0.0
S4 classes for QTL summary statistics and metadata2 versions - Latest release: 7 months ago - 1 dependent package - 840 downloads total - 1 stars on GitHub - 1 maintainer
phantasus 1.22.2
Visual and interactive gene expression analysis3 versions - Latest release: 6 months ago - 11 thousand downloads total - 1 maintainer
surfaltr 1.8.0
Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr3 versions - Latest release: 6 months ago - 2.28 thousand downloads total - 1 maintainer
BSgenomeForge 1.2.3
Forge BSgenome data packages5 versions - Latest release: about 1 month ago - 1 dependent package - 8.28 thousand downloads total - 1 maintainer
GenomicDistributions 1.10.0
GenomicDistributions: fast analysis of genomic intervals with Bioconductor3 versions - Latest release: 6 months ago - 4.62 thousand downloads total - 1 maintainer
CTDquerier 2.10.0
Package for CTDbase data query, visualization and downstream analysis3 versions - Latest release: 6 months ago - 5.56 thousand downloads total - 1 maintainer
CrispRVariants 1.30.0
Tools for counting and visualising mutations in a target location3 versions - Latest release: 6 months ago - 17.1 thousand downloads total - 1 maintainer
alabaster.spatial 1.2.0
Save and Load Spatial 'Omics Data to/from File3 versions - Latest release: 6 months ago - 1 dependent package - 1.85 thousand downloads total - 1 maintainer
SingleMoleculeFootprinting 1.10.0
Analysis tools for Single Molecule Footprinting (SMF) data3 versions - Latest release: 6 months ago - 2.89 thousand downloads total - 2 stars on GitHub - 1 maintainer
SparseArray 1.2.4
High-performance sparse data representation and manipulation in R5 versions - Latest release: 3 months ago - 5 dependent packages - 570 thousand downloads total - 1 maintainer
alabaster.ranges 1.2.0
Load and Save Ranges-related Artifacts from File3 versions - Latest release: 6 months ago - 2 dependent packages - 5.42 thousand downloads total - 1 maintainer
DelayedTensor 1.8.0
R package for sparse and out-of-core arithmetic and decomposition of Tensor3 versions - Latest release: 6 months ago - 2.52 thousand downloads total - 4 stars on GitHub - 1 maintainer
TreeAndLeaf 1.14.0
Displaying binary trees with focus on dendrogram leaves3 versions - Latest release: 6 months ago - 1 dependent package - 6.98 thousand downloads total - 1 maintainer
Spaniel 1.16.0
Spatial Transcriptomics Analysis3 versions - Latest release: 6 months ago - 6.46 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 39.9 thousand downloads total - 1 maintainer
interactiveDisplay 1.40.0
Package for enabling powerful shiny web displays of Bioconductor objects3 versions - Latest release: 6 months ago - 1 dependent package - 39.9 thousand downloads total - 1 maintainer
SpatialOmicsOverlay 1.2.1
Spatial Overlay for Omic Data from Nanostring GeoMx Data3 versions - Latest release: 6 months ago - 1.68 thousand downloads total - 1 maintainer
R4RNA 1.30.0
An R package for RNA visualization and analysis3 versions - Latest release: 6 months ago - 2 dependent packages - 30 thousand downloads total - 1 maintainer
ExperimentSubset 1.12.0
Manages subsets of data with Bioconductor Experiment objects3 versions - Latest release: 6 months ago - 3.77 thousand downloads total - 1 maintainer
updateObject 1.6.0
Find/fix old serialized S4 instances3 versions - Latest release: 6 months ago - 1.83 thousand downloads total - 1 maintainer
SCArray 1.10.0
Large-scale single-cell omics data manipulation with GDS files3 versions - Latest release: 6 months ago - 1 dependent package - 3.48 thousand downloads total - 1 stars on GitHub - 1 maintainer
nearBynding 1.12.0
Discern RNA structure proximal to protein binding3 versions - Latest release: 6 months ago - 3.5 thousand downloads total - 1 maintainer
alabaster.matrix 1.2.0
Load and Save Artifacts from File3 versions - Latest release: 6 months ago - 2 dependent packages - 5.74 thousand downloads total - 1 maintainer
alabaster.mae 1.2.0
Load and Save MultiAssayExperiments3 versions - Latest release: 6 months ago - 1 dependent package - 1.88 thousand downloads total - 1 maintainer
alabaster.vcf 1.2.0
Save and Load Variant Data to/from File3 versions - Latest release: 6 months ago - 1 dependent package - 1.8 thousand downloads total - 1 maintainer
alabaster.schemas 1.2.0
Schemas for the Alabaster Framework3 versions - Latest release: 6 months ago - 1 dependent package - 6.05 thousand downloads total - 1 maintainer
alabaster.sce 1.2.0
Load and Save SingleCellExperiment from File3 versions - Latest release: 6 months ago - 2 dependent packages - 3.03 thousand downloads total - 1 maintainer
alabaster.se 1.2.0
Load and Save SummarizedExperiments from File3 versions - Latest release: 6 months ago - 4 dependent packages - 5.5 thousand downloads total - 1 maintainer
flowPlots 1.50.0
flowPlots: analysis plots and data class for gated flow cytometry data3 versions - Latest release: 6 months ago - 23.7 thousand downloads total - 1 maintainer
Top 6.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 45.4 thousand downloads total - 1 maintainer
DEP 1.24.0
Differential Enrichment analysis of Proteomics data3 versions - Latest release: 6 months ago - 1 dependent package - 45.4 thousand downloads total - 1 maintainer
CellTrails 1.20.0
Reconstruction, visualization and analysis of branching trajectories3 versions - Latest release: 6 months ago - 6.81 thousand downloads total - 1 maintainer
psygenet2r 1.34.1
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric...4 versions - Latest release: 4 months ago - 11.5 thousand downloads total - 1 maintainer
Top 7.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 33.5 thousand downloads total - 1 maintainer
Rcpi 1.38.0
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery3 versions - Latest release: 6 months ago - 1 dependent package - 33.5 thousand downloads total - 1 maintainer
RImmPort 1.30.0
RImmPort: Enabling Ready-for-analysis Immunology Research Data3 versions - Latest release: 6 months ago - 9.87 thousand downloads total - 2 maintainers
MultimodalExperiment 1.2.0
Integrative Bulk and Single-Cell Experiment Container3 versions - Latest release: 6 months ago - 1.15 thousand downloads total - 1 maintainer
Top 7.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 36.6 thousand downloads total - 1 maintainer
flowDensity 1.36.1
Sequential Flow Cytometry Data Gating3 versions - Latest release: 6 months ago - 3 dependent packages - 36.6 thousand downloads total - 1 maintainer
Top 9.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 26.8 thousand downloads total - 1 maintainer
R453Plus1Toolbox 1.52.0
A package for importing and analyzing data from Roche's Genome Sequencer System3 versions - Latest release: 6 months ago - 26.8 thousand downloads total - 1 maintainer
NeuCA 1.8.1
NEUral network-based single-Cell Annotation tool4 versions - Latest release: 2 months ago - 2.02 thousand downloads total - 1 maintainer
weitrix 1.14.0
Tools for matrices with precision weights, test and explore weighted or sparse data3 versions - Latest release: 6 months ago - 4.22 thousand downloads total - 1 maintainer
chromPlot 1.30.0
Global visualization tool of genomic data3 versions - Latest release: 6 months ago - 16 thousand downloads total - 1 maintainer
MACSQuantifyR 1.16.0
Fast treatment of MACSQuantify FACS data3 versions - Latest release: 6 months ago - 4.32 thousand downloads total - 1 maintainer
LoomExperiment 1.20.0
LoomExperiment container3 versions - Latest release: 6 months ago - 2 dependent packages - 28.2 thousand downloads total - 1 maintainer
TVTB 1.28.0
TVTB: The VCF Tool Box3 versions - Latest release: 6 months ago - 9.85 thousand downloads total - 2 stars on GitHub - 1 maintainer
SCArray.sat 1.2.1
Large-scale single-cell RNA-seq data analysis using GDS files and Seurat4 versions - Latest release: 4 months ago - 1.24 thousand downloads total - 1 stars on GitHub - 1 maintainer
DepecheR 1.18.0
Determination of essential phenotypic elements of clusters in high-dimensional entities3 versions - Latest release: 6 months ago - 1 dependent package - 16 thousand downloads total - 1 maintainer
pipeComp 1.12.0
pipeComp pipeline benchmarking framework3 versions - Latest release: 6 months ago - 3.99 thousand downloads total - 1 maintainer
esetVis 1.28.2
Visualizations of expressionSet Bioconductor object4 versions - Latest release: 4 months ago - 12.3 thousand downloads total - 1 maintainer
alabaster.bumpy 1.2.0
Save and Load BumpyMatrices to/from file3 versions - Latest release: 6 months ago - 1 dependent package - 1.85 thousand downloads total - 1 maintainer
flowSpecs 1.16.0
Tools for processing of high-dimensional cytometry data3 versions - Latest release: 6 months ago - 5.55 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 9.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 13 dependent packages - 48.1 thousand downloads total - 1 maintainer
TreeSummarizedExperiment 2.10.0
TreeSummarizedExperiment: a S4 Class for Data with Tree Structures3 versions - Latest release: 6 months ago - 13 dependent packages - 48.1 thousand downloads total - 1 maintainer
Omixer 1.12.0
Omixer: multivariate and reproducible sample randomization to proactively counter batch effects i...3 versions - Latest release: 6 months ago - 3.65 thousand downloads total - 1 maintainer
oposSOM 2.20.0
Comprehensive analysis of transcriptome data3 versions - Latest release: 6 months ago - 17.7 thousand downloads total - 1 maintainer
Modstrings 1.18.0
Working with modified nucleotide sequences3 versions - Latest release: 6 months ago - 4 dependent packages - 10.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
MultiBaC 1.12.0
Multiomic Batch effect Correction3 versions - Latest release: 6 months ago - 4.52 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
3 versions - Latest release: 22 days ago - 45 dependent packages - 1.11 million downloads total - 15 stars on GitHub - 1 maintainer
DelayedMatrixStats 1.26.0
Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects3 versions - Latest release: 22 days ago - 45 dependent packages - 1.11 million downloads total - 15 stars on GitHub - 1 maintainer
cmapR 1.14.0
CMap Tools in R3 versions - Latest release: 6 months ago - 21.4 thousand downloads total - 78 stars on GitHub - 1 maintainer
doseR 1.18.0
doseR3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
Top 8.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 28.1 thousand downloads total - 1 maintainer
SplicingGraphs 1.42.0
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them3 versions - Latest release: 6 months ago - 28.1 thousand downloads total - 1 maintainer
PhIPData 1.10.0
Container for PhIP-Seq Experiments3 versions - Latest release: 6 months ago - 1 dependent package - 3.92 thousand downloads total - 2 stars on GitHub - 1 maintainer
alabaster.base 1.2.1
Save Bioconductor Objects To File3 versions - Latest release: 6 months ago - 11 dependent packages - 6.61 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 27.2 thousand downloads total - 86 stars on GitHub - 1 maintainer
scmap 1.24.0
A tool for unsupervised projection of single cell RNA-seq data3 versions - Latest release: 6 months ago - 27.2 thousand downloads total - 86 stars on GitHub - 1 maintainer
BaseSpaceR 1.46.0
R SDK for BaseSpace RESTful API3 versions - Latest release: 6 months ago - 23.8 thousand downloads total - 1 maintainer
phemd 1.18.0
Phenotypic EMD for comparison of single-cell samples3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
BumpyMatrix 1.10.0
Bumpy Matrix of Non-Scalar Objects3 versions - Latest release: 6 months ago - 10 dependent packages - 19.6 thousand downloads total - 1 maintainer
KEGGlincs 1.28.0
Visualize all edges within a KEGG pathway and overlay LINCS data3 versions - Latest release: 6 months ago - 10.9 thousand downloads total - 2 maintainers
consensus 1.20.0
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method3 versions - Latest release: 6 months ago - 6.17 thousand downloads total - 1 maintainer
VCFArray 1.18.0
Representing on-disk / remote VCF files as array-like objects3 versions - Latest release: 6 months ago - 5.81 thousand downloads total - 1 stars on GitHub - 1 maintainer
ipdDb 1.20.0
IPD IMGT/HLA and IPD KIR database for Homo sapiens3 versions - Latest release: 6 months ago - 6.95 thousand downloads total - 0 stars on GitHub - 1 maintainer
alabaster 1.2.0
Umbrella for the Alabaster Framework3 versions - Latest release: 6 months ago - 1.32 thousand downloads total - 1 maintainer
alabaster.string 1.2.0
Save and Load Biostrings to/from File3 versions - Latest release: 6 months ago - 2 dependent packages - 1.99 thousand downloads total - 1 maintainer
cytoMEM 1.6.0
Marker Enrichment Modeling (MEM)3 versions - Latest release: 6 months ago - 2.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
ImmuneSpaceR 1.30.0
A Thin Wrapper around the ImmuneSpace Data and Tools Portal3 versions - Latest release: 6 months ago - 12.2 thousand downloads total - 25 stars on GitHub - 1 maintainer
DeepBlueR 1.27.0 removed
DeepBlueR2 versions - Latest release: 6 months ago - 12.8 thousand downloads total - 3 maintainers
Top 4.0% on bioconductor.org
3 versions - Latest release: 6 days ago - 3 dependent packages - 92.8 thousand downloads total - 27 stars on GitHub - 1 maintainer
CytoML 2.16.0
A GatingML Interface for Cross Platform Cytometry Data Sharing3 versions - Latest release: 6 days ago - 3 dependent packages - 92.8 thousand downloads total - 27 stars on GitHub - 1 maintainer
DelayedRandomArray 1.12.0
Delayed Arrays of Random Values3 versions - Latest release: 7 days ago - 1 dependent package - 3.54 thousand downloads total - 0 stars on GitHub - 1 maintainer
SpatialFeatureExperiment 1.6.1
Integrating SpatialExperiment with Simple Features in sf4 versions - Latest release: 12 days ago - 1 dependent package - 4.09 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
7 versions - Latest release: 8 days ago - 11 dependent packages - 86.6 thousand downloads total - 42 stars on GitHub - 1 maintainer
SeqArray 1.44.0
Data Management of Large-Scale Whole-Genome Sequence Variant Calls7 versions - Latest release: 8 days ago - 11 dependent packages - 86.6 thousand downloads total - 42 stars on GitHub - 1 maintainer
Related Keywords
Software
148
DataImport
69
Infrastructure
58
Visualization
43
Sequencing
37
GeneExpression
28
ImmunoOncology
27
SingleCell
25
RNASeq
22
Clustering
19
Transcriptomics
18
Annotation
15
Genetics
15
Preprocessing
14
DifferentialExpression
12
QualityControl
12
MultipleComparison
11
DimensionReduction
11
Transcription
11
Coverage
11
FlowCytometry
10
Classification
10
GUI
9
Microarray
8
r
8
Network
8
Alignment
8
GenomeAnnotation
8
Pathways
7
GO
7
bioconductor
7
Normalization
7
SequenceMatching
6
ThirdPartyClient
6
BiomedicalInformatics
6
SystemsBiology
5
GraphAndNetwork
5
PrincipalComponent
5
GeneSetEnrichment
5
CellBasedAssays
5
Proteomics
5
Spatial
5
CellBiology
5
FunctionalGenomics
5
bioinformatics
5
bioconductor-package
5
KEGG
4
DNASeq
4
VariantAnnotation
4
ExperimentalDesign
4
GenomicVariation
3
DNAMethylation
3
FeatureExtraction
3
MultipleSequenceAlignment
3
human-cell-atlas
3
GeneticVariability
3
Epigenetics
3
Regression
3
GeneRegulation
3
HiC
3
TimeCourse
3
shiny
2
AnnotationData
2
r-package
2
ShinyApps
2
GeneTarget
2
GenotypingArray
2
ATACSeq
2
Bioinformatics
2
HighThroughputSequencing
2
single-cell-rna-seq
2
SupportVectorMachine
2
BatchEffect
2
sequences
2
rna
2
SNP
2
cancer-genomics
2
BiologicalQuestion
2
GenomeAssembly
2
AlternativeSplicing
2
Survival
2
clinical-data
1
cbioportal
1
mutations
1
data-structure
1
core-package
1
copynumber
1
fhir
1
tcga
1
DNaseSeq
1
DNA3DStructure
1
ChIPSeq
1
maf-files
1
grammar
1
genomic-data-analysis
1
genomes
1
data-manipulation
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biconductor
1
WorkflowStep
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rmarkdown
1