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bioconductor.org "Software" keyword

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

fCCAC 1.36.0
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing ...
6 versions - Latest release: 2 months ago - 16.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.88.0
Annotation for microarrays
7 versions - Latest release: 3 months ago - 48 dependent packages - 4.71 million downloads total - 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: 3 months ago - 10 dependent packages - 405 thousand downloads total - 1 maintainer
Rfastp 1.20.2
An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX ...
7 versions - Latest release: about 3 hours ago - 14.9 thousand downloads total - 1 maintainer
GIGSEA 1.28.0
Genotype Imputed Gene Set Enrichment Analysis
6 versions - Latest release: 2 months ago - 11.3 thousand downloads total - 1 maintainer
brendaDb 1.24.0
The BRENDA Enzyme Database
6 versions - Latest release: 2 months ago - 11.5 thousand downloads total - 2 stars on GitHub - 1 maintainer
EnMCB 1.22.0
Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models
6 versions - Latest release: 3 months ago - 10.8 thousand downloads total - 9 stars on GitHub - 1 maintainer
MIRit 1.6.1
Integrate microRNA and gene expression to decipher pathway complexity
8 versions - Latest release: about 2 months ago - 5.94 thousand downloads total - 1 stars on GitHub - 1 maintainer
CleanUpRNAseq 1.4.0
Detect and Correct Genomic DNA Contamination in RNA-seq Data
3 versions - Latest release: 2 months ago - 3.67 thousand downloads total - 1 maintainer
benchdamic 1.16.0
Benchmark of differential abundance methods on microbiome data
13 versions - Latest release: 2 months ago - 7.68 thousand downloads total - 5 stars on GitHub - 1 maintainer
scHOT 1.22.0
single-cell higher order testing
6 versions - Latest release: 2 months ago - 11.4 thousand downloads total - 1 maintainer
Top 10.0% on bioconductor.org
CAGEr 2.16.0
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcr...
6 versions - Latest release: 2 months ago - 2 dependent packages - 46.8 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
phyloseq 1.54.0
Handling and analysis of high-throughput microbiome census data
6 versions - Latest release: 3 months ago - 23 dependent packages - 1.07 million downloads total - 1 maintainer
rexposome 1.32.0
Exposome exploration and outcome data analysis
6 versions - Latest release: 2 months ago - 1 dependent package - 19.2 thousand downloads total - 1 maintainer
BOBaFIT 1.14.0
Refitting diploid region profiles using a clustering procedure
6 versions - Latest release: 2 months ago - 7.99 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.0% on bioconductor.org
ROC 1.86.0
utilities for ROC, with microarray focus
6 versions - Latest release: 3 months ago - 6 dependent packages - 317 thousand downloads total - 1 maintainer
cmapR 1.22.0
CMap Tools in R
6 versions - Latest release: 3 months ago - 46.4 thousand downloads total - 92 stars on GitHub - 1 maintainer
tidyomics 1.6.0
Easily install and load the tidyomics ecosystem
5 versions - Latest release: 2 months ago - 5.59 thousand downloads total - 68 stars on GitHub - 1 maintainer
PhyloProfile 2.2.2
PhyloProfile
16 versions - Latest release: 2 months ago - 15.3 thousand downloads total - 37 stars on GitHub - 1 maintainer
ExploreModelMatrix 1.22.0
Graphical Exploration of Design Matrices
7 versions - Latest release: 2 months ago - 19.2 thousand downloads total - 37 stars on GitHub - 1 maintainer
universalmotif 1.28.0
Import, Modify, and Export Motifs with R
9 versions - Latest release: 2 months ago - 4 dependent packages - 77.5 thousand downloads total - 1 maintainer
spatzie 1.15.1
Identification of enriched motif pairs from chromatin interaction data
6 versions - Latest release: 2 months ago - 7.02 thousand downloads total - 1 maintainer
HVP 1.0.0
Hierarchical Variance Partitioning
1 version - Latest release: 3 months ago - 1.38 thousand downloads total - 1 maintainer
CardinalIO 1.8.0
Read and write mass spectrometry imaging files
5 versions - Latest release: 3 months ago - 1 dependent package - 10.6 thousand 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: 3 months ago - 96 dependent packages - 1.05 million downloads total - 1 maintainer
transite 1.28.0
RNA-binding protein motif analysis
8 versions - Latest release: 3 months ago - 13 thousand downloads total - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.78.0
Efficient manipulation of biological strings
11 versions - Latest release: 3 months ago - 333 dependent packages - 9.32 million downloads total - 1 maintainer
funOmics 1.4.0
Aggregating Omics Data into Higher-Level Functional Representations
3 versions - Latest release: 3 months ago - 3.79 thousand downloads total - 6 stars on GitHub - 1 maintainer
velociraptor 1.20.0
Toolkit for Single-Cell Velocity
7 versions - Latest release: 3 months ago - 16 thousand downloads total - 59 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.54.1
R Interface to HDF5
11 versions - Latest release: 2 months ago - 69 dependent packages - 3.25 million downloads total - 69 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
TrajectoryUtils 1.18.0
Single-Cell Trajectory Analysis Utilities
8 versions - Latest release: 2 months ago - 5 dependent packages - 174 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: 3 months ago - 31 dependent packages - 938 thousand downloads total - 64 stars on GitHub - 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: 3 months ago - 45 dependent packages - 5.39 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: 3 months ago - 740 dependent packages - 11.1 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
zlibbioc 1.54.0 removed
An R packaged zlib-1.2.5
6 versions - Latest release: 10 months ago - 29 dependent packages - 8.95 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
enrichplot 1.30.4
Visualization of Functional Enrichment Result
20 versions - Latest release: 2 months ago - 15 dependent packages - 2.2 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.78.0
Get data from NCBI Gene Expression Omnibus (GEO)
6 versions - Latest release: 3 months ago - 47 dependent packages - 2.33 million downloads total - 103 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: 3 months ago - 9 dependent packages - 333 thousand downloads total - 481 stars on GitHub - 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: about 1 month ago - 181 dependent packages - 4.24 million downloads total - 4 maintainers
Top 0.1% on bioconductor.org
BiocGenerics 0.56.0
S4 generic functions used in Bioconductor
7 versions - Latest release: 3 months ago - 729 dependent packages - 11.9 million downloads total - 1 maintainer
kmcut 1.4.0
Optimized Kaplan Meier analysis and identification and validation of prognostic biomarkers
3 versions - Latest release: 3 months ago - 3.36 thousand downloads total - 1 maintainer
compSPOT 1.8.0
compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots
5 versions - Latest release: 3 months ago - 5.28 thousand downloads total - 0 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: 3 months ago - 27 dependent packages - 2.19 million downloads total - 1 maintainer
Top 1.8% on bioconductor.org
seqLogo 1.76.0
Sequence logos for DNA sequence alignments
6 versions - Latest release: 3 months ago - 15 dependent packages - 505 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.88.0
Methods for Affymetrix Oligonucleotide Arrays
6 versions - Latest release: 3 months ago - 74 dependent packages - 2.24 million downloads total - 1 maintainer
Top 7.6% on bioconductor.org
Mulcom 1.60.0
Calculates Mulcom test
6 versions - Latest release: 3 months ago - 40.4 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: 3 months ago - 183 dependent packages - 4.27 million downloads total - 1 maintainer
IVAS 2.30.0
Identification of genetic Variants affecting Alternative Splicing
6 versions - Latest release: 2 months ago - 1 dependent package - 21.7 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.58.0
Surrogate Variable Analysis
7 versions - Latest release: 3 months ago - 43 dependent packages - 1.16 million downloads total - 3 maintainers
Top 1.5% on bioconductor.org
EnhancedVolcano 1.28.2
Publication-ready volcano plots with enhanced colouring and labeling
7 versions - Latest release: 2 months ago - 494 thousand downloads total - 384 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: 3 months ago - 129 dependent packages - 2.77 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: 3 months ago - 54 dependent packages - 1.71 million downloads total - 1 maintainer
Top 8.6% on bioconductor.org
flagme 1.66.0
Analysis of Metabolomics GC/MS Data
6 versions - Latest release: 2 months ago - 36.9 thousand downloads total - 2 maintainers
Top 1.7% on bioconductor.org
vsn 3.78.1
Variance stabilization and calibration for microarray data
7 versions - Latest release: 19 days ago - 30 dependent packages - 1.17 million downloads total - 1 maintainer
findIPs 1.6.0
Influential Points Detection for Feature Rankings
4 versions - Latest release: 3 months ago - 4.77 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.68.0
FASTQ input and manipulation
7 versions - Latest release: 3 months ago - 36 dependent packages - 1.97 million downloads total - 1 maintainer
MPRAnalyze 1.28.0
Statistical Analysis of MPRA data
6 versions - Latest release: 2 months ago - 13.3 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
qvalue 2.42.0
Q-value estimation for false discovery rate control
6 versions - Latest release: 3 months ago - 45 dependent packages - 2.37 million downloads total - 106 stars on GitHub - 2 maintainers
Top 1.4% on bioconductor.org
GSEABase 1.72.0
Gene set enrichment data structures and methods
7 versions - Latest release: 3 months ago - 49 dependent packages - 1.38 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: 2 months ago - 13 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: 3 months ago - 201 dependent packages - 2 million downloads total - 1 maintainer
RNAsense 1.24.0
Analysis of Time-Resolved RNA-Seq Data
6 versions - Latest release: 2 months ago - 10.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.1% on bioconductor.org
BiocParallel 1.44.0
Bioconductor facilities for parallel evaluation
10 versions - Latest release: 3 months ago - 377 dependent packages - 8.68 million downloads total - 63 stars on GitHub - 1 maintainer
BUMHMM 1.34.0
Computational pipeline for computing probability of modification from structure probing experimen...
6 versions - Latest release: 2 months ago - 16.7 thousand downloads total - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.36.2
Fast Gene Set Enrichment Analysis
10 versions - Latest release: about 1 month ago - 38 dependent packages - 2.24 million downloads total - 345 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
Rsubread 2.24.0
Mapping, quantification and variant analysis of sequencing data
8 versions - Latest release: 3 months ago - 14 dependent packages - 415 thousand downloads total - 2 maintainers
Top 1.9% on bioconductor.org
MSnbase 2.36.0
Base Functions and Classes for Mass Spectrometry and Proteomics
8 versions - Latest release: 3 months ago - 30 dependent packages - 587 thousand downloads total - 123 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
VariantAnnotation 1.56.0
Annotation of Genetic Variants
8 versions - Latest release: 3 months ago - 93 dependent packages - 2.06 million downloads total - 1 maintainer
PANR 1.56.0
Posterior association networks and functional modules inferred from rich phenotypes of gene pertu...
6 versions - Latest release: 2 months ago - 29 thousand downloads total - 1 maintainer
MethReg 1.20.0
Assessing the regulatory potential of DNA methylation regions or sites on gene transcription
7 versions - Latest release: 2 months ago - 10.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
methylPipe 1.44.0
Base resolution DNA methylation data analysis
7 versions - Latest release: 2 months ago - 1 dependent package - 29.7 thousand downloads total - 1 maintainer
peakPantheR 1.24.0
Peak Picking and Annotation of High Resolution Experiments
8 versions - Latest release: 3 months ago - 11.5 thousand downloads total - 12 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: 3 months ago - 132 dependent packages - 4.89 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
impute 1.84.0
impute: Imputation for microarray data
6 versions - Latest release: 3 months ago - 44 dependent packages - 1.96 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: 3 months ago - 563 dependent packages - 11.6 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.54.0
Provides plotting capabilities for R graph objects
6 versions - Latest release: 3 months ago - 61 dependent packages - 1.92 million downloads total - 1 maintainer
GRENITS 1.62.0
Gene Regulatory Network Inference Using Time Series
6 versions - Latest release: 2 months ago - 30 thousand 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: 3 months ago - 15 dependent packages - 970 thousand downloads total - 185 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
RBGL 1.86.0
An interface to the BOOST graph library
6 versions - Latest release: 3 months ago - 33 dependent packages - 1.91 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
multtest 2.66.0
Resampling-based multiple hypothesis testing
6 versions - Latest release: 3 months ago - 37 dependent packages - 2.62 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: 3 months ago - 146 dependent packages - 4.17 million downloads total - 330 stars on GitHub - 1 maintainer
Top 0.1% on bioconductor.org
Biobase 2.70.0
Biobase: Base functions for Bioconductor
6 versions - Latest release: 3 months ago - 518 dependent packages - 11.1 million downloads total - 1 maintainer
Top 2.6% on bioconductor.org
ConsensusClusterPlus 1.74.0
ConsensusClusterPlus
6 versions - Latest release: 2 months ago - 7 dependent packages - 441 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: 3 months ago - 12 dependent packages - 438 thousand 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 1 month ago - 51 dependent packages - 4.95 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: 2 months ago - 342 dependent packages - 10.6 million downloads total - 1 maintainer
Top 0.7% on bioconductor.org
graph 1.88.1
graph: A package to handle graph data structures
8 versions - Latest release: 2 months ago - 101 dependent packages - 3.46 million downloads total - 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: about 2 months ago - 251 dependent packages - 5.11 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: 3 months ago - 36 dependent packages - 9.36 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
ggtree 4.0.4
an R package for visualization of tree and annotation data
12 versions - Latest release: about 1 month ago - 28 dependent packages - 2.22 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: 2 months ago - 604 dependent packages - 9.23 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: about 2 months ago - 59 dependent packages - 2.37 million downloads total - 1 maintainer
specL 1.44.0
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
6 versions - Latest release: 2 months ago - 23.4 thousand 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: 3 months ago - 322 dependent packages - 6.92 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: 3 months ago - 111 dependent packages - 7.73 million downloads total - 1 maintainer
DeepTarget 1.4.0
Deep characterization of cancer drugs
3 versions - Latest release: 3 months ago - 3.75 thousand downloads total - 1 maintainer
SDAMS 1.30.0
Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequen...
6 versions - Latest release: 2 months ago - 14 thousand downloads total - 1 maintainer
MOGAMUN 1.20.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
6 versions - Latest release: 3 months ago - 9.75 thousand downloads total - 12 stars on GitHub - 1 maintainer
flowMeans 1.70.0
Non-parametric Flow Cytometry Data Gating
6 versions - Latest release: 2 months ago - 2 dependent packages - 58.4 thousand downloads total - 1 maintainer
Top 8.7% on bioconductor.org
regionReport 1.44.0
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
6 versions - Latest release: 2 months ago - 1 dependent package - 36.7 thousand downloads total - 10 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 200 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 FeatureExtraction 69 KEGG 69 NetworkInference 69 DifferentialMethylation 67 TwoChannel 64 TimeCourse 61 Microbiome 60 PrincipalComponent 58 GenomeAnnotation 58 bioconductor-package 58 SequenceMatching 57 NetworkEnrichment 57 GeneTarget 56 AlternativeSplicing 55 Survival 47 WorkflowStep 47 GeneticVariability 47 MethylationArray 47 ReportWriting 44 DNASeq 44 rstats 43 WholeGenome 43 GenomicVariation 43 GenomeWideAssociation 41 Metagenomics 41 ShinyApps 41 MethylSeq 40 ThirdPartyClient 39 ATACSeq 39 DifferentialSplicing 39 VariantAnnotation 37 ExperimentalDesign 36 r-package 35 FunctionalPrediction 35 BiologicalQuestion 35 HiC 35 GenePrediction 31 Reactome 30 Technology 29 mRNAMicroarray 28 genomics 28 SomaticMutation 28 mass-spectrometry 27 PeakDetection 27 CRISPR 26 MotifAnnotation 25