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bioconductor.org "Software" keyword

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

spARI 1.0.0
Spatially Aware Adjusted Rand Index for Evaluating Spatial Transcritpomics Clustering
1 version - Latest release: 2 months ago - 662 downloads total - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.54.1
R Interface to HDF5
11 versions - Latest release: 29 days ago - 69 dependent packages - 3.18 million downloads total - 69 stars on GitHub - 1 maintainer
gpuMagic 1.25.1
An openCL compiler with the capacity to compile R functions and run the code on GPU
6 versions - Latest release: 2 months ago - 10.3 thousand downloads total - 10 stars on GitHub - 1 maintainer
seqArchRplus 1.9.0
Downstream analyses of promoter sequence architectures and HTML report generation
6 versions - Latest release: about 1 month ago - 5.73 thousand downloads total - 1 stars on GitHub - 1 maintainer
iscream 1.0.0
Make fast and memory efficient BED file queries, summaries and matrices
1 version - Latest release: 2 months ago - 483 downloads total - 0 stars on GitHub - 1 maintainer
Top 0.1% on bioconductor.org
BiocGenerics 0.56.0
S4 generic functions used in Bioconductor
7 versions - Latest release: 2 months ago - 729 dependent packages - 11.7 million downloads total - 1 maintainer
scDotPlot 1.4.0
Cluster a Single-cell RNA-seq Dot Plot
5 versions - Latest release: about 1 month ago - 4.42 thousand downloads total - 7 stars on GitHub - 1 maintainer
SpaNorm 1.4.0
Spatially-aware normalisation for spatial transcriptomics data
3 versions - Latest release: about 1 month ago - 3.68 thousand downloads total - 13 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: 2 months ago - 96 dependent packages - 1.03 million downloads total - 1 maintainer
GIGSEA 1.28.0
Genotype Imputed Gene Set Enrichment Analysis
6 versions - Latest release: about 1 month ago - 11 thousand downloads total - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.56.0
Analyze Illumina Infinium DNA methylation arrays
8 versions - Latest release: 2 months ago - 31 dependent packages - 930 thousand downloads total - 64 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.62.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
6 versions - Latest release: 2 months ago - 10 dependent packages - 402 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.72.0
Gene set enrichment data structures and methods
7 versions - Latest release: 2 months ago - 49 dependent packages - 1.36 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
GenomeInfoDb 1.46.2
Utilities for manipulating chromosome names, including modifying them to follow a particular nami...
21 versions - Latest release: 29 days ago - 342 dependent packages - 10.5 million downloads total - 1 maintainer
CeTF 1.22.0
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation an...
6 versions - Latest release: about 1 month ago - 12.6 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
qvalue 2.42.0
Q-value estimation for false discovery rate control
6 versions - Latest release: 2 months ago - 45 dependent packages - 2.32 million downloads total - 106 stars on GitHub - 2 maintainers
Top 0.7% on bioconductor.org
graph 1.88.1
graph: A package to handle graph data structures
8 versions - Latest release: 26 days ago - 101 dependent packages - 3.41 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
VariantAnnotation 1.56.0
Annotation of Genetic Variants
8 versions - Latest release: 2 months ago - 93 dependent packages - 2.03 million downloads total - 1 maintainer
soGGi 1.41.1
Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Gen...
7 versions - Latest release: about 1 month ago - 1 dependent package - 44 thousand downloads total - 1 maintainer
Top 0.7% on bioconductor.org
genefilter 1.92.0
genefilter: methods for filtering genes from high-throughput experiments
6 versions - Latest release: 2 months ago - 66 dependent packages - 4.11 million downloads total - 1 maintainer
compcodeR 1.46.0
RNAseq data simulation, differential expression analysis and performance comparison of differenti...
6 versions - Latest release: about 1 month ago - 32.4 thousand downloads total - 12 stars on GitHub - 1 maintainer
multistateQTL 2.2.0
Toolkit for the analysis of multi-state QTL data
5 versions - Latest release: about 2 months ago - 4.55 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.78.0
Get data from NCBI Gene Expression Omnibus (GEO)
6 versions - Latest release: 2 months ago - 47 dependent packages - 2.3 million downloads total - 103 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
ggtree 4.0.3
an R package for visualization of tree and annotation data
11 versions - Latest release: 15 days ago - 28 dependent packages - 2.14 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.88.0
Methods for Affymetrix Oligonucleotide Arrays
6 versions - Latest release: 2 months ago - 74 dependent packages - 2.22 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: 2 months ago - 36 dependent packages - 9.2 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.8.0
LC-MS and GC-MS Data Analysis
13 versions - Latest release: 2 months ago - 15 dependent packages - 962 thousand downloads total - 185 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: 2 months ago - 129 dependent packages - 2.73 million downloads total - 1 maintainer
LoomExperiment 1.28.0
LoomExperiment container
7 versions - Latest release: about 1 month ago - 2 dependent packages - 47.8 thousand downloads total - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.8.2
Empirical Analysis of Digital Gene Expression Data in R
26 versions - Latest release: 8 days ago - 181 dependent packages - 4.18 million downloads total - 4 maintainers
Top 1.0% on bioconductor.org
Rgraphviz 2.54.0
Provides plotting capabilities for R graph objects
6 versions - Latest release: 2 months ago - 61 dependent packages - 1.9 million downloads total - 1 maintainer
cola 2.16.0
A Framework for Consensus Partitioning
6 versions - Latest release: 2 months ago - 2 dependent packages - 21.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.78.0
Efficient manipulation of biological strings
11 versions - Latest release: 2 months ago - 333 dependent packages - 9.17 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
EnhancedVolcano 1.28.2
Publication-ready volcano plots with enhanced colouring and labeling
7 versions - Latest release: 29 days ago - 481 thousand downloads total - 384 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: 2 months ago - 563 dependent packages - 11.4 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.58.0
Surrogate Variable Analysis
7 versions - Latest release: 2 months ago - 43 dependent packages - 1.14 million downloads total - 3 maintainers
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: 2 months ago - 45 dependent packages - 5.27 million downloads total - 1 maintainer
RNAsense 1.24.0
Analysis of Time-Resolved RNA-Seq Data
6 versions - Latest release: about 1 month ago - 9.76 thousand downloads total - 1 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: 26 days ago - 604 dependent packages - 9.08 million downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.66.0
Linear Models for Microarray and Omics Data
16 versions - Latest release: 2 months ago - 322 dependent packages - 6.83 million downloads total - 1 maintainer
Top 2.0% on bioconductor.org
ROC 1.86.0
utilities for ROC, with microarray focus
6 versions - Latest release: 2 months ago - 6 dependent packages - 311 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
RBGL 1.86.0
An interface to the BOOST graph library
6 versions - Latest release: 2 months ago - 33 dependent packages - 1.88 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.88.0
Annotation for microarrays
7 versions - Latest release: 2 months ago - 48 dependent packages - 4.66 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
clusterProfiler 4.18.4
A universal enrichment tool for interpreting omics data
19 versions - Latest release: 20 days ago - 59 dependent packages - 2.31 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
Biobase 2.70.0
Biobase: Base functions for Bioconductor
6 versions - Latest release: 2 months ago - 518 dependent packages - 11 million 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: 2 months ago - 632 dependent packages - 7.5 million downloads total - 1 maintainer
Top 1.1% on bioconductor.org
BiocParallel 1.44.0
Bioconductor facilities for parallel evaluation
10 versions - Latest release: 2 months ago - 377 dependent packages - 8.53 million downloads total - 63 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
maftools 2.26.0 💰
Summarize, Analyze and Visualize MAF Files
6 versions - Latest release: 2 months ago - 9 dependent packages - 327 thousand downloads total - 481 stars on GitHub - 1 maintainer
Top 1.3% on bioconductor.org
impute 1.84.0
impute: Imputation for microarray data
6 versions - Latest release: 2 months ago - 44 dependent packages - 1.94 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
enrichplot 1.30.4
Visualization of Functional Enrichment Result
20 versions - Latest release: about 1 month ago - 15 dependent packages - 2.14 million downloads total - 1 maintainer
scPCA 1.24.0
Sparse Contrastive Principal Component Analysis
6 versions - Latest release: 2 months ago - 13.7 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 4.4.0
Disease Ontology Semantic and Enrichment analysis
13 versions - Latest release: 2 months ago - 27 dependent packages - 2.13 million downloads total - 1 maintainer
Top 0.8% on bioconductor.org
flowCore 2.22.0
flowCore: Basic structures for flow cytometry data
8 versions - Latest release: 2 months ago - 51 dependent packages - 4.94 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
DESeq2 1.50.2
Differential gene expression analysis based on the negative binomial distribution
11 versions - Latest release: about 2 months ago - 146 dependent packages - 4.1 million downloads total - 330 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
seqLogo 1.76.0
Sequence logos for DNA sequence alignments
6 versions - Latest release: 2 months ago - 15 dependent packages - 497 thousand downloads total - 4 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: 2 months ago - 30 dependent packages - 575 thousand downloads total - 123 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: 2 months ago - 132 dependent packages - 4.82 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.68.0
FASTQ input and manipulation
7 versions - Latest release: 2 months ago - 36 dependent packages - 1.95 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.36.0
Fast Gene Set Enrichment Analysis
9 versions - Latest release: 2 months ago - 38 dependent packages - 2.17 million downloads total - 345 stars on GitHub - 1 maintainer
Top 0.4% on bioconductor.org
rtracklayer 1.70.1
R interface to genome annotation files and the UCSC genome browser
7 versions - Latest release: 11 days ago - 251 dependent packages - 5.04 million downloads total - 1 maintainer
affyILM 1.62.0
Linear Model of background subtraction and the Langmuir isotherm
6 versions - Latest release: about 1 month ago - 39.4 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
DropletUtils 1.30.0
Utilities for Handling Single-Cell Droplet Data
7 versions - Latest release: about 1 month ago - 14 dependent packages - 313 thousand downloads total - 1 maintainer
brendaDb 1.24.0
The BRENDA Enzyme Database
6 versions - Latest release: about 1 month ago - 11.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
POMA 1.20.0
Tools for Omics Data Analysis
6 versions - Latest release: about 2 months ago - 1 dependent package - 14.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
DiffBind 3.20.0
Differential Binding Analysis of ChIP-Seq Peak Data
6 versions - Latest release: about 1 month ago - 2 dependent packages - 299 thousand downloads total - 1 maintainer
specL 1.44.0
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
6 versions - Latest release: about 1 month ago - 22.9 thousand 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: 2 months ago - 183 dependent packages - 4.22 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
vsn 3.78.0
Variance stabilization and calibration for microarray data
6 versions - Latest release: 2 months ago - 30 dependent packages - 1.15 million 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: 2 months ago - 12 dependent packages - 432 thousand 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: 2 months ago - 54 dependent packages - 1.67 million downloads total - 1 maintainer
Top 4.1% on bioconductor.org
makecdfenv 1.86.0
CDF Environment Maker
6 versions - Latest release: about 1 month ago - 1 dependent package - 89.1 thousand 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: 2 months ago - 111 dependent packages - 7.6 million downloads total - 1 maintainer
Top 3.3% on bioconductor.org
ChIPseeker 1.46.1
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
7 versions - Latest release: about 1 month ago - 6 dependent packages - 350 thousand downloads total - 1 maintainer
BloodGen3Module 1.18.0
This R package for performing module repertoire analyses and generating fingerprint representations
6 versions - Latest release: about 1 month ago - 10.5 thousand downloads total - 1 maintainer
XeniumIO 1.2.0
Import and represent Xenium data from the 10X Xenium Analyzer
2 versions - Latest release: about 1 month ago - 2.38 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.2% on bioconductor.org
multtest 2.66.0
Resampling-based multiple hypothesis testing
6 versions - Latest release: 2 months ago - 37 dependent packages - 2.59 million downloads total - 1 maintainer
ExploreModelMatrix 1.22.0
Graphical Exploration of Design Matrices
7 versions - Latest release: about 1 month ago - 18.6 thousand downloads total - 37 stars on GitHub - 1 maintainer
pram 1.26.0
Pooling RNA-seq datasets for assembling transcript models
6 versions - Latest release: about 1 month ago - 10.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
RNAmodR.RiboMethSeq 1.24.0
Detection of 2'-O methylations by RiboMethSeq
6 versions - Latest release: about 1 month ago - 10.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
adductomicsR 1.26.0
Processing of adductomic mass spectral datasets
6 versions - Latest release: about 1 month ago - 15 thousand downloads total - 1 stars on GitHub - 1 maintainer
MGFR 1.35.0
Marker Gene Finder in RNA-seq data
6 versions - Latest release: about 1 month ago - 1 dependent package - 16.4 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
Rsubread 2.24.0
Mapping, quantification and variant analysis of sequencing data
8 versions - Latest release: 2 months ago - 14 dependent packages - 411 thousand downloads total - 2 maintainers
Top 9.0% on bioconductor.org
illuminaio 0.52.0
Parsing Illumina Microarray Output Files
6 versions - Latest release: about 1 month ago - 12 dependent packages - 579 thousand downloads total - 5 stars on GitHub - 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: 2 months ago - 740 dependent packages - 10.9 million downloads total - 1 maintainer
Top 5.1% on bioconductor.org
ACME 2.66.0
Algorithms for Calculating Microarray Enrichment (ACME)
6 versions - Latest release: about 1 month ago - 1 dependent package - 53.7 thousand downloads total - 1 maintainer
IVAS 2.30.0
Identification of genetic Variants affecting Alternative Splicing
6 versions - Latest release: about 1 month ago - 1 dependent package - 21.2 thousand downloads total - 1 maintainer
Top 7.0% on bioconductor.org
SCAN.UPC 2.52.0
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
6 versions - Latest release: about 1 month ago - 43.6 thousand downloads total - 1 maintainer
PathNet 1.50.0
An R package for pathway analysis using topological information
6 versions - Latest release: about 1 month ago - 27.1 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
GenomicInteractions 1.44.0
Utilities for handling genomic interaction data
6 versions - Latest release: about 1 month ago - 7 dependent packages - 69.3 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
SingleCellExperiment 1.32.0
S4 Classes for Single Cell Data
8 versions - Latest release: 2 months ago - 201 dependent packages - 1.94 million downloads total - 1 maintainer
FastqCleaner 1.28.0
A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
6 versions - Latest release: about 1 month ago - 16.2 thousand downloads total - 1 maintainer
fastreeR 2.0.0
Phylogenetic, Distance and Other Calculations on VCF and Fasta Files
8 versions - Latest release: about 1 month ago - 8.57 thousand downloads total - 24 stars on GitHub - 1 maintainer
CompoundDb 1.14.0
Creating and Using (Chemical) Compound Annotation Databases
7 versions - Latest release: about 1 month ago - 3 dependent packages - 28.2 thousand downloads total - 19 stars on GitHub - 1 maintainer
Top 9.0% on bioconductor.org
maCorrPlot 1.80.0
Visualize artificial correlation in microarray data
6 versions - Latest release: about 1 month ago - 34.7 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
diffGeneAnalysis 1.92.0
Performs differential gene expression Analysis
6 versions - Latest release: about 1 month ago - 35.9 thousand downloads total - 1 maintainer
zenith 1.12.0
Gene set analysis following differential expression using linear (mixed) modeling with dream
7 versions - Latest release: about 1 month ago - 2 dependent packages - 11.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.8% on bioconductor.org
fabia 2.56.0
FABIA: Factor Analysis for Bicluster Acquisition
6 versions - Latest release: about 1 month ago - 3 dependent packages - 58.4 thousand downloads total - 1 maintainer
GUIDEseq 1.40.0
GUIDE-seq and PEtag-seq analysis pipeline
6 versions - Latest release: about 1 month ago - 1 dependent package - 21.8 thousand downloads total - 1 maintainer
Melissa 1.25.0
Bayesian clustering and imputationa of single cell methylomes
6 versions - Latest release: about 1 month ago - 10.7 thousand downloads total - 1 maintainer
nipalsMCIA 1.8.0
Multiple Co-Inertia Analysis via the NIPALS Method
9 versions - Latest release: about 2 months ago - 5.9 thousand downloads total - 7 stars on GitHub - 1 maintainer
Related Keywords
GeneExpression 664 Sequencing 659 Visualization 482 ImmunoOncology 460 RNASeq 438 DifferentialExpression 420 Microarray 375 DataImport 368 SingleCell 341 Clustering 320 Transcriptomics 297 Preprocessing 290 Infrastructure 269 QualityControl 255 Genetics 227 Proteomics 208 Transcription 199 Classification 195 MultipleComparison 194 Network 189 Normalization 189 StatisticalMethod 183 GeneSetEnrichment 179 Coverage 175 Pathways 168 DataRepresentation 167 Regression 157 MassSpectrometry 156 Annotation 156 GraphAndNetwork 151 r 130 bioconductor 127 Metabolomics 125 DNAMethylation 124 GeneRegulation 123 SystemsBiology 112 FunctionalGenomics 109 Alignment 107 Epigenetics 106 ChIPSeq 100 Bayesian 98 BiomedicalInformatics 96 SNP 96 DimensionReduction 94 GO 84 Spatial 80 BatchEffect 79 CopyNumberVariation 78 bioinformatics 75 FlowCytometry 73 CellBasedAssays 73 CellBiology 72 OneChannel 72 GUI 71 NetworkInference 69 FeatureExtraction 69 KEGG 69 DifferentialMethylation 67 TwoChannel 64 TimeCourse 61 Microbiome 60 PrincipalComponent 58 GenomeAnnotation 58 SequenceMatching 57 bioconductor-package 57 NetworkEnrichment 57 GeneTarget 56 AlternativeSplicing 55 WorkflowStep 47 GeneticVariability 47 Survival 47 MethylationArray 47 DNASeq 44 ReportWriting 44 rstats 43 GenomicVariation 43 WholeGenome 43 GenomeWideAssociation 41 Metagenomics 41 ShinyApps 41 MethylSeq 40 ThirdPartyClient 39 DifferentialSplicing 39 ATACSeq 39 VariantAnnotation 37 ExperimentalDesign 36 FunctionalPrediction 35 BiologicalQuestion 35 HiC 35 r-package 34 GenePrediction 31 Reactome 30 Technology 29 mRNAMicroarray 28 SomaticMutation 28 genomics 28 PeakDetection 27 CRISPR 26 mass-spectrometry 26 MotifAnnotation 25