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bioconductor.org "Classification" keyword

MEB 1.26.0
A normalization-invariant minimum enclosing ball method to detect differentially expressed genes ...
7 versions - Latest release: about 2 hours ago - 12.5 thousand downloads total - 2 maintainers
Top 6.3% on bioconductor.org
gpls 1.84.0
Classification using generalized partial least squares
7 versions - Latest release: about 10 hours ago - 1 dependent package - 70.9 thousand downloads total - 1 maintainer
PIUMA 1.8.0
Phenotypes Identification Using Mapper from topological data Analysis
6 versions - Latest release: about 10 hours ago - 5.82 thousand downloads total - 5 stars on GitHub - 1 maintainer
RGSEA 1.46.0
Random Gene Set Enrichment Analysis
7 versions - Latest release: about 12 hours ago - 26.8 thousand downloads total - 1 maintainer
sigFeature 1.30.0
sigFeature: Significant feature selection using SVM-RFE & t-statistic
7 versions - Latest release: about 18 hours ago - 26.5 thousand downloads total - 1 maintainer
NuPoP 2.20.0
An R package for nucleosome positioning prediction
7 versions - Latest release: about 23 hours ago - 1 dependent package - 34 thousand downloads total
adverSCarial 1.10.0
adverSCarial, generate and analyze the vulnerability of scRNA-seq classifier to adversarial attacks
6 versions - Latest release: 1 day ago - 6.84 thousand downloads total - 1 maintainer
clstutils 1.60.0
Tools for performing taxonomic assignment
7 versions - Latest release: 1 day ago - 32.4 thousand downloads total - 1 maintainer
rRDP 1.44.0 removed
Interface to the RDP Classifier
6 versions - Latest release: 6 months ago - 22.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
maftools 2.28.0 💰
Summarize, Analyze and Visualize MAF Files
7 versions - Latest release: 22 days ago - 9 dependent packages - 349 thousand downloads total - 492 stars on GitHub - 1 maintainer
Ibex 1.2.0
Methods for BCR single-cell embedding
3 versions - Latest release: 2 days ago - 1.45 thousand downloads total - 25 stars on GitHub - 1 maintainer
survClust 1.6.0
Identification Of Clinically Relevant Genomic Subtypes Using Outcome Weighted Learning
4 versions - Latest release: 2 days ago - 4.77 thousand downloads total - 16 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
phyloseq 1.56.0
Handling and analysis of high-throughput microbiome census data
8 versions - Latest release: 3 days ago - 23 dependent packages - 1.12 million downloads total - 1 maintainer
biosigner 1.40.0
Signature discovery from omics data
8 versions - Latest release: 3 days ago - 2 dependent packages - 25.4 thousand downloads total - 1 maintainer
katdetectr 1.14.0
Detection, Characterization and Visualization of Kataegis in Sequencing Data
7 versions - Latest release: 3 days ago - 8.91 thousand downloads total - 1 maintainer
microbiomeExplorer 1.22.0
Microbiome Exploration App
7 versions - Latest release: 3 days ago - 15.2 thousand downloads total - 1 maintainer
antiProfiles 1.52.0
Implementation of gene expression anti-profiles
7 versions - Latest release: 4 days ago - 31.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
interactiveDisplayBase 1.48.0 removed
Base package for enabling powerful shiny web displays of Bioconductor objects
6 versions - Latest release: 6 months ago - 3 dependent packages - 1.03 million downloads total - 1 maintainer
ORFhunteR 1.20.0
Predict open reading frames in nucleotide sequences
7 versions - Latest release: 4 days ago - 10.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
rexposome 1.34.2
Exposome exploration and outcome data analysis
8 versions - Latest release: 4 days ago - 1 dependent package - 21.8 thousand downloads total - 1 maintainer
Top 6.8% on bioconductor.org
vbmp 1.80.0
Variational Bayesian Multinomial Probit Regression
7 versions - Latest release: 4 days ago - 45 thousand downloads total - 1 maintainer
POMA 1.22.0
Tools for Omics Data Analysis
7 versions - Latest release: 4 days ago - 1 dependent package - 17 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
made4 1.86.0
Multivariate analysis of microarray data using ADE4
7 versions - Latest release: 4 days ago - 1 dependent package - 108 thousand downloads total - 1 maintainer
BreastSubtypeR 1.4.0
Cohort-aware methods for intrinsic molecular subtyping of breast cancer
3 versions - Latest release: 4 days ago - 3.63 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.6% on bioconductor.org
mixOmics 6.36.0
Omics Data Integration Project
7 versions - Latest release: 4 days ago - 9 dependent packages - 383 thousand downloads total - 1 maintainer
evaluomeR 1.28.0
Evaluation of Bioinformatics Metrics
8 versions - Latest release: 4 days ago - 13.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
ctc 1.86.0
Cluster and Tree Conversion.
7 versions - Latest release: 4 days ago - 2 dependent packages - 107 thousand downloads total - 1 maintainer
demuxmix 1.14.0
Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models
7 versions - Latest release: 5 days ago - 1 dependent package - 13.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
partCNV 1.9.0
Infer locally aneuploid cells using single cell RNA-seq data
6 versions - Latest release: 5 days ago - 6.59 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
MLSeq 2.30.0
Machine Learning Interface for RNA-Seq Data
7 versions - Latest release: 6 days ago - 1 dependent package - 40.7 thousand downloads total - 1 maintainer
CAEN 1.20.0
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
7 versions - Latest release: 6 days ago - 9.54 thousand downloads total - 1 maintainer
spatzie 1.18.0
Identification of enriched motif pairs from chromatin interaction data
7 versions - Latest release: 6 days ago - 7.69 thousand downloads total - 1 maintainer
Top 3.5% on bioconductor.org
dada2 1.40.0
Accurate, high-resolution sample inference from amplicon sequencing data
7 versions - Latest release: 6 days ago - 2 dependent packages - 908 thousand downloads total - 530 stars on GitHub - 1 maintainer
SIAMCAT 2.16.0
Statistical Inference of Associations between Microbial Communities And host phenoTypes
7 versions - Latest release: 6 days ago - 23.3 thousand downloads total - 1 maintainer
SubCellBarCode 1.28.0
SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
7 versions - Latest release: 6 days ago - 13.1 thousand downloads total - 1 maintainer
MethPed 1.40.0
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
7 versions - Latest release: 6 days ago - 19.2 thousand downloads total - 1 maintainer
scClassify 1.24.0
scClassify: single-cell Hierarchical Classification
7 versions - Latest release: 6 days ago - 15.3 thousand downloads total - 20 stars on GitHub - 1 maintainer
CONFESS 1.40.0
Cell OrderiNg by FluorEScence Signal
7 versions - Latest release: 6 days ago - 20.3 thousand downloads total - 1 maintainer
rScudo 1.28.0
Signature-based Clustering for Diagnostic Purposes
8 versions - Latest release: 7 days ago - 13.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
ggtreeDendro 1.14.0
Drawing 'dendrogram' using 'ggtree'
7 versions - Latest release: 7 days ago - 8.28 thousand downloads total - 1 maintainer
bandle 1.16.0
An R package for the Bayesian analysis of differential subcellular localisation experiments
7 versions - Latest release: 7 days ago - 9.85 thousand downloads total - 4 stars on GitHub - 1 maintainer
MAI 1.18.0
Mechanism-Aware Imputation
7 versions - Latest release: 7 days ago - 13.3 thousand downloads total - 2 stars on GitHub - 1 maintainer
ClustIRR 1.10.0
Clustering of Immune Receptor Repertoires
6 versions - Latest release: 7 days ago - 7.05 thousand downloads total - 5 stars on GitHub - 1 maintainer
COSNet 1.46.0
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
7 versions - Latest release: 7 days ago - 23 thousand downloads total - 1 stars on GitHub
massiR 1.48.0
massiR: MicroArray Sample Sex Identifier
7 versions - Latest release: 8 days ago - 26.4 thousand downloads total - 1 maintainer
easier 1.18.0
Estimate Systems Immune Response from RNA-seq data
7 versions - Latest release: 8 days ago - 13.4 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
procoil 2.40.0
Prediction of Oligomerization of Coiled Coil Proteins
7 versions - Latest release: 8 days ago - 40.3 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
CRImage 1.60.0
CRImage a package to classify cells and calculate tumour cellularity
7 versions - Latest release: 9 days ago - 44.2 thousand downloads total - 2 maintainers
consensusOV 1.34.0
Gene expression-based subtype classification for high-grade serous ovarian cancer
7 versions - Latest release: 9 days ago - 1 dependent package - 19.4 thousand downloads total - 1 maintainer
CytoDx 1.32.0
Robust prediction of clinical outcomes using cytometry data without cell gating
7 versions - Latest release: 9 days ago - 16.5 thousand downloads total - 1 maintainer
Top 3.0% on bioconductor.org
metagenomeSeq 1.54.0
Statistical analysis for sparse high-throughput sequencing
8 versions - Latest release: 9 days ago - 11 dependent packages - 257 thousand downloads total - 71 stars on GitHub - 1 maintainer
Top 6.3% on bioconductor.org
CMA 1.70.0
Synthesis of microarray-based classification
7 versions - Latest release: 9 days ago - 60.9 thousand downloads total - 1 maintainer
PAA 1.46.0
PAA (Protein Array Analyzer)
7 versions - Latest release: 9 days ago - 28.1 thousand downloads total - 2 maintainers
ROCpAI 1.24.0
Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers
7 versions - Latest release: 9 days ago - 10.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
decontam 1.32.0
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
7 versions - Latest release: 9 days ago - 1 dependent package - 151 thousand downloads total - 163 stars on GitHub - 1 maintainer
maPredictDSC 1.50.0
Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Dia...
7 versions - Latest release: 9 days ago - 26.5 thousand downloads total - 1 maintainer
ClusterSignificance 1.40.0
The ClusterSignificance package provides tools to assess if class clusters in dimensionality redu...
7 versions - Latest release: 9 days ago - 19.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
compSPOT 1.10.0
compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots
6 versions - Latest release: 10 days ago - 6.24 thousand downloads total - 0 stars on GitHub - 1 maintainer
GARS 1.32.0
GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional...
7 versions - Latest release: 10 days ago - 16.5 thousand downloads total - 1 maintainer
geNetClassifier 1.52.0
Classify diseases and build associated gene networks using gene expression profiles
7 versions - Latest release: 10 days ago - 2 dependent packages - 38.5 thousand downloads total - 1 maintainer
RadioGx 2.16.0
Analysis of Large-Scale Radio-Genomic Data
7 versions - Latest release: 10 days ago - 13.7 thousand downloads total - 1 maintainer
rfPred 1.50.0
Assign rfPred functional prediction scores to a missense variants list
7 versions - Latest release: 11 days ago - 27.1 thousand downloads total - 1 maintainer
KnowSeq 1.25.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
7 versions - Latest release: 11 days ago - 15.4 thousand downloads total - 1 maintainer
SigCheck 2.44.0
Check a gene signature's prognostic performance against random signatures, known signatures, and ...
7 versions - Latest release: 11 days ago - 22.9 thousand downloads total - 1 maintainer
iNETgrate 1.10.0
Integrates DNA methylation data with gene expression in a single gene network
7 versions - Latest release: 11 days ago - 6.87 thousand downloads total - 65 stars on GitHub - 1 maintainer
Top 8.9% on bioconductor.org
kebabs 1.46.0
Kernel-Based Analysis of Biological Sequences
7 versions - Latest release: 11 days ago - 2 dependent packages - 46.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.3% on bioconductor.org
AIMS 1.44.0
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
7 versions - Latest release: 11 days ago - 1 dependent package - 76.4 thousand downloads total - 1 maintainer
Xeva 1.28.0
Analysis of patient-derived xenograft (PDX) data
8 versions - Latest release: 11 days ago - 15.1 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 8.8% on bioconductor.org
iterativeBMA 1.70.0
The Iterative Bayesian Model Averaging (BMA) algorithm
7 versions - Latest release: 11 days ago - 38.3 thousand downloads total - 1 maintainer
LedPred 1.46.0
Learning from DNA to Predict Enhancers
7 versions - Latest release: 11 days ago - 18.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
clst 1.60.0
Classification by local similarity threshold
7 versions - Latest release: 11 days ago - 1 dependent package - 34.1 thousand downloads total - 1 maintainer
DaMiRseq 2.24.0
Data Mining for RNA-seq data: normalization, feature selection and classification
7 versions - Latest release: 11 days ago - 1 dependent package - 24.1 thousand downloads total - 1 maintainer
BadRegionFinder 1.39.0
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
7 versions - Latest release: 11 days ago - 21.3 thousand downloads total - 1 maintainer
escape 2.8.0
Easy single cell analysis platform for enrichment
10 versions - Latest release: 11 days ago - 1 dependent package - 38.9 thousand downloads total - 1 maintainer
Top 4.5% on bioconductor.org
genefu 2.42.0
Computation of Gene Expression-Based Signatures in Breast Cancer
6 versions - Latest release: 6 months ago - 3 dependent packages - 95 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
EGSEA 1.40.0
Ensemble of Gene Set Enrichment Analyses
8 versions - Latest release: 12 days ago - 1 dependent package - 42.9 thousand downloads total - 1 maintainer
SVMDO 1.11.0
Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by D...
10 versions - Latest release: 12 days ago - 8.31 thousand downloads total - 0 stars on GitHub - 1 maintainer
TTMap 1.34.0
Two-Tier Mapper: a clustering tool based on topological data analysis
7 versions - Latest release: 12 days ago - 15.8 thousand downloads total - 1 maintainer
graper 1.28.0
Adaptive penalization in high-dimensional regression and classification with external covariates ...
8 versions - Latest release: 12 days ago - 13.3 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
bioDist 1.84.0
Different distance measures
7 versions - Latest release: 12 days ago - 2 dependent packages - 106 thousand downloads total - 1 maintainer
nipalsMCIA 1.10.0
Multiple Co-Inertia Analysis via the NIPALS Method
11 versions - Latest release: 12 days ago - 7.63 thousand downloads total - 7 stars on GitHub - 1 maintainer
XAItest 1.4.0
XAItest: Enhancing Feature Discovery with eXplainable AI
6 versions - Latest release: 12 days ago - 3.44 thousand downloads total - 1 stars on GitHub - 1 maintainer
LinkHD 1.26.0
LinkHD: a versatile framework to explore and integrate heterogeneous data
7 versions - Latest release: 12 days ago - 12.4 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
DirichletMultinomial 1.54.0
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
7 versions - Latest release: 13 days ago - 5 dependent packages - 527 thousand downloads total - 10 stars on GitHub - 1 maintainer
scds 2.0.0
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
8 versions - Latest release: 13 days ago - 2 dependent packages - 64.1 thousand downloads total - 1 maintainer
Cepo 1.18.0
Cepo for the identification of differentially stable genes
8 versions - Latest release: 13 days ago - 1 dependent package - 15.4 thousand downloads total - 1 maintainer
DeMixT 2.0.0
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components usin...
7 versions - Latest release: 13 days ago - 16.7 thousand downloads total - 1 maintainer
SemDist 1.46.0
Information Accretion-based Function Predictor Evaluation
7 versions - Latest release: 13 days ago - 22.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.8% on bioconductor.org
phenoTest 1.60.0
Tools to test association between gene expression and phenotype in a way that is efficient, struc...
7 versions - Latest release: 14 days ago - 1 dependent package - 44.3 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
MLInterfaces 1.92.0
Uniform interfaces to R machine learning procedures for data in Bioconductor containers
8 versions - Latest release: 14 days ago - 2 dependent packages - 134 thousand downloads total - 1 maintainer
PLSDAbatch 2.0.0
PLSDA-batch
5 versions - Latest release: 14 days ago - 6.42 thousand downloads total - 13 stars on GitHub - 1 maintainer
cancerclass 1.56.0
Development and validation of diagnostic tests from high-dimensional molecular data
7 versions - Latest release: 14 days ago - 39.9 thousand downloads total - 1 maintainer
immApex 1.6.0
Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning
10 versions - Latest release: 14 days ago - 8.67 thousand downloads total - 12 stars on GitHub - 1 maintainer
HiCPotts 1.2.0
HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C
2 versions - Latest release: 14 days ago - 1.86 thousand downloads total - 0 stars on GitHub - 1 maintainer
ssPATHS 1.26.0
ssPATHS: Single Sample PATHway Score
7 versions - Latest release: 14 days ago - 11.7 thousand downloads total - 1 maintainer
CNVPanelizer 1.44.0
Reliable CNV detection in targeted sequencing applications
7 versions - Latest release: 14 days ago - 24.9 thousand downloads total - 1 maintainer
iCOBRA 1.40.0
Comparison and Visualization of Ranking and Assignment Methods
7 versions - Latest release: 14 days ago - 2 dependent packages - 46.1 thousand downloads total - 16 stars on GitHub - 1 maintainer
SGCP 1.11.1
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...
10 versions - Latest release: 14 days ago - 7.94 thousand downloads total - 2 stars on GitHub - 1 maintainer
lefser 1.22.0
R implementation of the LEfSE method for microbiome biomarker discovery
9 versions - Latest release: 15 days ago - 1 dependent package - 96.8 thousand downloads total - 42 stars on GitHub - 1 maintainer
fgga 1.20.0
Hierarchical ensemble method based on factor graph
8 versions - Latest release: 15 days ago - 10.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
Related Keywords
Software 206 GeneExpression 65 Clustering 63 Sequencing 54 ImmunoOncology 41 SingleCell 36 RNASeq 35 Microarray 35 Visualization 34 Transcriptomics 34 DifferentialExpression 30 MultipleComparison 25 StatisticalMethod 24 FeatureExtraction 24 Regression 24 Survival 18 Proteomics 17 Genetics 17 Preprocessing 17 Normalization 17 Network 16 DataImport 16 QualityControl 15 DimensionReduction 15 Annotation 15 GeneSetEnrichment 14 Pathways 14 Transcription 13 GraphAndNetwork 13 Microbiome 13 FunctionalGenomics 12 SystemsBiology 12 Metagenomics 12 BiomedicalInformatics 12 PrincipalComponent 11 DataRepresentation 11 SupportVectorMachine 10 Bayesian 10 Epigenetics 9 bioinformatics 9 Metabolomics 9 MassSpectrometry 9 GenePrediction 8 GO 8 r 8 bioconductor 8 Coverage 7 Alignment 7 CellBiology 7 Pharmacogenomics 6 SNP 6 CopyNumberVariation 5 NetworkInference 5 ChIPSeq 5 HiddenMarkovModel 5 ShinyApps 5 GUI 5 BatchEffect 5 Pharmacogenetics 5 WholeGenome 5 Lipidomics 5 r-package 5 GeneticVariability 5 Infrastructure 5 DNASeq 5 DNAMethylation 4 FlowCytometry 4 PeakDetection 4 CellBasedAssays 4 rstats 4 NeuralNetwork 4 HiC 4 Spatial 4 GenomeWideAssociation 4 GeneSignaling 4 DecisionTree 4 MotifAnnotation 3 KEGG 3 GeneTarget 3 MathematicalBiology 3 transcriptomics 3 GenomeAnnotation 3 OneChannel 3 bioconductor-package 3 metagenomics 3 GenomicVariation 3 ddPCR 3 GeneRegulation 3 single-cell-rna-seq 3 WorkflowStep 3 DNA3DStructure 3 ATACSeq 3 machine-learning 3 ExperimentalDesign 3 mRNAMicroarray 3 Technology 3 SequenceMatching 3 SomaticMutation 3 ExperimentHubSoftware 2 AnnotationData 2