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bioconductor.org "Classification" keyword

adverSCarial 1.8.0
adverSCarial, generate and analyze the vulnerability of scRNA-seq classifier to adversarial attacks
5 versions - Latest release: 3 months ago - 5.86 thousand downloads total - 1 maintainer
Pigengene 1.35.0
Infers biological signatures from gene expression data
6 versions - Latest release: 3 months ago - 1 dependent package - 21.3 thousand downloads total - 1 maintainer
Top 4.4% on bioconductor.org
SingleR 2.12.0
Reference-Based Single-Cell RNA-Seq Annotation
7 versions - Latest release: 3 months ago - 5 dependent packages - 396 thousand downloads total - 196 stars on GitHub - 1 maintainer
CytoDx 1.30.0
Robust prediction of clinical outcomes using cytometry data without cell gating
6 versions - Latest release: 3 months ago - 15.1 thousand downloads total - 1 maintainer
Top 5.2% on bioconductor.org
pRoloc 1.50.0
A unifying bioinformatics framework for spatial proteomics
8 versions - Latest release: 4 months ago - 3 dependent packages - 82.6 thousand downloads total - 16 stars on GitHub - 1 maintainer
rRDP 1.44.0
Interface to the RDP Classifier
6 versions - Latest release: 4 months ago - 21.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
DeMixT 1.26.0
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components usin...
6 versions - Latest release: 3 months ago - 15.3 thousand downloads total - 1 maintainer
Top 7.8% on bioconductor.org
phenoTest 1.58.0
Tools to test association between gene expression and phenotype in a way that is efficient, struc...
6 versions - Latest release: 3 months ago - 1 dependent package - 42.3 thousand downloads total - 1 maintainer
peco 1.22.0
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
6 versions - Latest release: 3 months ago - 10.4 thousand downloads total - 12 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: 4 months ago - 9 dependent packages - 336 thousand downloads total - 485 stars on GitHub - 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: 3 months ago - 3 dependent packages - 93.5 thousand downloads total - 1 maintainer
BreastSubtypeR 1.2.0
Cohort-aware methods for intrinsic molecular subtyping of breast cancer
2 versions - Latest release: 3 months ago - 2.87 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
interactiveDisplayBase 1.48.0
Base package for enabling powerful shiny web displays of Bioconductor objects
6 versions - Latest release: 3 months ago - 3 dependent packages - 1.03 million downloads total - 1 maintainer
Top 5.3% on bioconductor.org
bioDist 1.82.0
Different distance measures
6 versions - Latest release: 3 months ago - 2 dependent packages - 104 thousand downloads total - 1 maintainer
rScudo 1.26.0
Signature-based Clustering for Diagnostic Purposes
7 versions - Latest release: 4 months ago - 12.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 9.3% on bioconductor.org
AIMS 1.42.0
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
6 versions - Latest release: 3 months ago - 1 dependent package - 73.9 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
DirichletMultinomial 1.52.0
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
6 versions - Latest release: 3 months ago - 5 dependent packages - 503 thousand downloads total - 10 stars on GitHub - 1 maintainer
SVMDO 1.10.0
Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by D...
9 versions - Latest release: 3 months ago - 7.42 thousand downloads total - 0 stars on GitHub - 1 maintainer
cancerclass 1.54.0
Development and validation of diagnostic tests from high-dimensional molecular data
6 versions - Latest release: 3 months ago - 37.6 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
kebabs 1.44.0
Kernel-Based Analysis of Biological Sequences
6 versions - Latest release: 3 months ago - 2 dependent packages - 44.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
PAA 1.44.0
PAA (Protein Array Analyzer)
6 versions - Latest release: 3 months ago - 25.9 thousand downloads total - 2 maintainers
Top 9.2% on bioconductor.org
Rmagpie 1.66.0
MicroArray Gene-expression-based Program In Error rate estimation
6 versions - Latest release: 3 months ago - 34.9 thousand downloads total - 1 maintainer
ssPATHS 1.24.0
ssPATHS: Single Sample PATHway Score
6 versions - Latest release: 3 months ago - 10.5 thousand downloads total - 1 maintainer
SIAMCAT 2.14.0
Statistical Inference of Associations between Microbial Communities And host phenoTypes
6 versions - Latest release: 3 months ago - 21.8 thousand downloads total - 1 maintainer
escape 2.6.2
Easy single cell analysis platform for enrichment
9 versions - Latest release: 30 days ago - 1 dependent package - 36.4 thousand downloads total - 1 maintainer
a4Core 1.58.0
Automated Affymetrix Array Analysis Core Package
6 versions - Latest release: 3 months ago - 3 dependent packages - 53.6 thousand downloads total - 1 maintainer
semisup 1.34.0
Semi-Supervised Mixture Model
6 versions - Latest release: 3 months ago - 14.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
iNETgrate 1.8.0
Integrates DNA methylation data with gene expression in a single gene network
6 versions - Latest release: 30 days ago - 5.72 thousand downloads total - 65 stars on GitHub - 1 maintainer
lefser 1.20.2
R implementation of the LEfSE method for microbiome biomarker discovery
8 versions - Latest release: 3 months ago - 1 dependent package - 93.7 thousand downloads total - 42 stars on GitHub - 1 maintainer
ggtreeDendro 1.12.0
Drawing 'dendrogram' using 'ggtree'
6 versions - Latest release: 3 months ago - 7.36 thousand downloads total - 1 maintainer
massiR 1.46.0
massiR: MicroArray Sample Sex Identifier
6 versions - Latest release: 3 months ago - 24.6 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
MLInterfaces 1.90.0
Uniform interfaces to R machine learning procedures for data in Bioconductor containers
7 versions - Latest release: 3 months ago - 2 dependent packages - 130 thousand downloads total - 1 maintainer
Top 3.0% on bioconductor.org
metagenomeSeq 1.52.0
Statistical analysis for sparse high-throughput sequencing
7 versions - Latest release: 3 months ago - 11 dependent packages - 249 thousand downloads total - 71 stars on GitHub - 1 maintainer
bandle 1.14.0
An R package for the Bayesian analysis of differential subcellular localisation experiments
6 versions - Latest release: 3 months ago - 8.57 thousand downloads total - 4 stars on GitHub - 1 maintainer
TTMap 1.32.0
Two-Tier Mapper: a clustering tool based on topological data analysis
6 versions - Latest release: 3 months ago - 14.3 thousand downloads total - 1 maintainer
RadioGx 2.14.0
Analysis of Large-Scale Radio-Genomic Data
6 versions - Latest release: 3 months ago - 12.4 thousand downloads total - 1 maintainer
Top 5.7% on bioconductor.org
GenVisR 1.42.2
Genomic Visualizations in R
7 versions - Latest release: 30 days ago - 64.6 thousand downloads total - 194 stars on GitHub - 1 maintainer
MethPed 1.38.0
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
6 versions - Latest release: 3 months ago - 17.5 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
EGSEA 1.38.0
Ensemble of Gene Set Enrichment Analyses
7 versions - Latest release: 3 months ago - 1 dependent package - 40.1 thousand downloads total - 1 maintainer
DaMiRseq 2.22.0
Data Mining for RNA-seq data: normalization, feature selection and classification
6 versions - Latest release: 3 months ago - 1 dependent package - 22.1 thousand downloads total - 1 maintainer
biosigner 1.38.0
Signature discovery from omics data
7 versions - Latest release: 3 months ago - 2 dependent packages - 23.7 thousand downloads total - 1 maintainer
BadRegionFinder 1.38.0
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
6 versions - Latest release: 3 months ago - 19.7 thousand downloads total - 1 maintainer
CAEN 1.18.0
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
6 versions - Latest release: 3 months ago - 8.34 thousand downloads total - 1 maintainer
GARS 1.30.0
GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional...
6 versions - Latest release: 3 months ago - 15.1 thousand downloads total - 1 maintainer
PoDCall 1.18.0
Positive Droplet Calling for DNA Methylation Droplet Digital PCR
7 versions - Latest release: 3 months ago - 7.68 thousand downloads total - 1 maintainer
geneClassifiers 1.34.0
Application of gene classifiers
6 versions - Latest release: 3 months ago - 15.7 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
iterativeBMA 1.68.0
The Iterative Bayesian Model Averaging (BMA) algorithm
6 versions - Latest release: 3 months ago - 36.7 thousand downloads total - 1 maintainer
ClassifyR 3.14.0
A framework for cross-validated classification problems, with applications to differential variab...
22 versions - Latest release: 3 months ago - 4 dependent packages - 37.8 thousand downloads total - 5 stars on GitHub - 1 maintainer
pathwayPCA 1.26.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
6 versions - Latest release: 3 months ago - 1 dependent package - 15.2 thousand downloads total - 11 stars on GitHub - 1 maintainer
scds 1.26.1
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
7 versions - Latest release: 2 days ago - 2 dependent packages - 60 thousand downloads total - 1 maintainer
clst 1.58.0
Classification by local similarity threshold
6 versions - Latest release: 3 months ago - 1 dependent package - 32.6 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
CRImage 1.58.0
CRImage a package to classify cells and calculate tumour cellularity
6 versions - Latest release: 3 months ago - 42.1 thousand downloads total - 2 maintainers
Top 3.8% on bioconductor.org
ropls 1.42.0
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
6 versions - Latest release: 4 months ago - 9 dependent packages - 139 thousand downloads total - 1 maintainer
timeOmics 1.22.0
Time-Course Multi-Omics data integration
6 versions - Latest release: 4 months ago - 1 dependent package - 12.4 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
scmap 1.32.0
A tool for unsupervised projection of single cell RNA-seq data
6 versions - Latest release: 4 months ago - 49.3 thousand downloads total - 86 stars on GitHub - 1 maintainer
consICA 2.8.0
consensus Independent Component Analysis
6 versions - Latest release: 4 months ago - 8.87 thousand downloads total - 0 stars on GitHub - 1 maintainer
PROPS 1.32.0
PRObabilistic Pathway Score (PROPS)
7 versions - Latest release: 4 months ago - 14.6 thousand downloads total - 1 maintainer
cola 2.16.1
A Framework for Consensus Partitioning
7 versions - Latest release: 15 days ago - 2 dependent packages - 22.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
normr 1.36.0
Normalization and difference calling in ChIP-seq data
6 versions - Latest release: 3 months ago - 24.4 thousand downloads total - 11 stars on GitHub - 1 maintainer
DepecheR 1.26.0
Determination of essential phenotypic elements of clusters in high-dimensional entities
6 versions - Latest release: 4 months ago - 1 dependent package - 24.5 thousand downloads total - 1 maintainer
Top 4.4% on bioconductor.org
SC3 1.38.0
Single-Cell Consensus Clustering
6 versions - Latest release: 4 months ago - 4 dependent packages - 91.7 thousand downloads total - 128 stars on GitHub - 1 maintainer
miRNAtap 1.44.0
miRNAtap: microRNA Targets - Aggregated Predictions
6 versions - Latest release: 4 months ago - 1 dependent package - 32.6 thousand downloads total - 1 maintainer
iCOBRA 1.38.0
Comparison and Visualization of Ranking and Assignment Methods
6 versions - Latest release: 4 months ago - 2 dependent packages - 42.5 thousand downloads total - 16 stars on GitHub - 1 maintainer
HiCPotts 1.0.0
HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C
1 version - Latest release: 4 months ago - 799 downloads total - 0 stars on GitHub - 1 maintainer
simpleSeg 1.12.0
A package to perform simple cell segmentation
10 versions - Latest release: 3 months ago - 9.69 thousand downloads total - 0 stars on GitHub - 1 maintainer
Coralysis 1.0.0
Coralysis sensitive identification of imbalanced cell types and states in single-cell data via mu...
1 version - Latest release: 4 months ago - 1.85 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
fastseg 1.56.0
fastseg - a fast segmentation algorithm
6 versions - Latest release: 3 months ago - 1 dependent package - 151 thousand downloads total - 1 maintainer
evaluomeR 1.26.0
Evaluation of Bioinformatics Metrics
7 versions - Latest release: 3 months ago - 12.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
GrafGen 1.6.0
Classification of Helicobacter Pylori Genomes
4 versions - Latest release: 3 months ago - 4.9 thousand downloads total - 1 maintainer
doubletrouble 1.10.0
Identification and classification of duplicated genes
13 versions - Latest release: 3 months ago - 8.1 thousand downloads total - 31 stars on GitHub - 1 maintainer
Top 8.4% on bioconductor.org
gaga 2.56.0
GaGa hierarchical model for high-throughput data analysis
6 versions - Latest release: 4 months ago - 1 dependent package - 41.3 thousand downloads total - 1 maintainer
PDATK 1.18.0
Pancreatic Ductal Adenocarcinoma Tool-Kit
7 versions - Latest release: 4 months ago - 10 thousand downloads total - 1 stars on GitHub - 1 maintainer
demuxmix 1.12.0
Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models
6 versions - Latest release: 3 months ago - 1 dependent package - 12.5 thousand downloads total - 5 stars on GitHub - 1 maintainer
islify 1.2.0
Automatic scoring and classification of cell-based assay images
2 versions - Latest release: 4 months ago - 2.42 thousand downloads total - 1 maintainer
idr2d 1.24.0
Irreproducible Discovery Rate for Genomic Interactions Data
7 versions - Latest release: 3 months ago - 12.1 thousand downloads total - 1 maintainer
TrIdent 1.2.0
TrIdent - Transduction Identification
2 versions - Latest release: 4 months ago - 2.78 thousand downloads total - 2 stars on GitHub - 1 maintainer
glmSparseNet 1.28.0
Network Centrality Metrics for Elastic-Net Regularized Models
7 versions - Latest release: 3 months ago - 107 thousand downloads total - 3 stars on GitHub - 1 maintainer
decontam 1.30.0
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
6 versions - Latest release: 3 months ago - 1 dependent package - 141 thousand downloads total - 163 stars on GitHub - 1 maintainer
twoddpcr 1.34.0
Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules
6 versions - Latest release: 4 months ago - 16.1 thousand downloads total - 9 stars on GitHub - 1 maintainer
nipalsMCIA 1.8.1
Multiple Co-Inertia Analysis via the NIPALS Method
10 versions - Latest release: 13 days ago - 6.45 thousand downloads total - 7 stars on GitHub - 1 maintainer
nempi 1.18.0
Inferring unobserved perturbations from gene expression data
6 versions - Latest release: 3 months ago - 8.81 thousand downloads total - 2 stars on GitHub - 1 maintainer
PLSDAbatch 1.6.0
PLSDA-batch
4 versions - Latest release: 3 months ago - 5.5 thousand downloads total - 13 stars on GitHub - 1 maintainer
AlpsNMR 4.12.0
Automated spectraL Processing System for NMR
7 versions - Latest release: 3 months ago - 13.6 thousand downloads total - 16 stars on GitHub - 1 maintainer
squallms 1.4.0
Speedy quality assurance via lasso labeling for LC-MS data
3 versions - Latest release: 3 months ago - 3.58 thousand downloads total - 3 stars on GitHub - 1 maintainer
looking4clusters 1.0.0
Interactive Visualization of scRNA-Seq
1 version - Latest release: 4 months ago - 821 downloads total - 0 stars on GitHub - 1 maintainer
switchBox 1.46.0
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair ...
6 versions - Latest release: 3 months ago - 1 dependent package - 26.3 thousand downloads total - 3 maintainers
preciseTAD 1.20.0
preciseTAD: A machine learning framework for precise TAD boundary prediction
6 versions - Latest release: 3 months ago - 11.5 thousand downloads total - 8 stars on GitHub - 1 maintainer
RLSeq 1.6.0 removed
RLSeq: An analysis package for R-loop mapping data
3 versions - Latest release: over 2 years ago - 2.67 thousand downloads total - 2 stars on GitHub - 1 maintainer
demuxSNP 1.8.0
scRNAseq demultiplexing using cell hashing and SNPs
6 versions - Latest release: 4 months ago - 6.11 thousand downloads total - 7 stars on GitHub - 1 maintainer
pathMED 1.2.0
Scoring Personalized Molecular Portraits
4 versions - Latest release: 3 months ago - 2.06 thousand downloads total - 5 stars on GitHub - 1 maintainer
scReClassify 1.16.0
scReClassify: post hoc cell type classification of single-cell RNA-seq data
6 versions - Latest release: 3 months ago - 9.03 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 8.1% on bioconductor.org
MiPP 1.82.0
Misclassification Penalized Posterior Classification
6 versions - Latest release: 3 months ago - 38.7 thousand downloads total - 1 maintainer
Ibex 1.0.0
Methods for BCR single-cell embedding
2 versions - Latest release: 3 months ago - 586 downloads total - 25 stars on GitHub - 1 maintainer
markeR 1.0.0
An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
1 version - Latest release: 4 months ago - 854 downloads total - 7 stars on GitHub - 1 maintainer
scoup 1.4.0
Simulate Codons with Darwinian Selection Modelled as an OU Process
3 versions - Latest release: 3 months ago - 3.19 thousand downloads total - 0 stars on GitHub - 1 maintainer
SemDist 1.44.0
Information Accretion-based Function Predictor Evaluation
6 versions - Latest release: 4 months ago - 20.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
SCFA 1.20.0
SCFA: Subtyping via Consensus Factor Analysis
6 versions - Latest release: 4 months ago - 9.05 thousand downloads total - 3 stars on GitHub - 1 maintainer
MAI 1.16.0
Mechanism-Aware Imputation
6 versions - Latest release: 4 months ago - 8.29 thousand downloads total - 2 stars on GitHub - 1 maintainer
Statial 1.12.0
A package to identify changes in cell state relative to spatial associations
10 versions - Latest release: 3 months ago - 8.71 thousand downloads total - 6 stars on GitHub - 1 maintainer
GPA 1.22.0
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
6 versions - Latest release: 3 months ago - 9.65 thousand downloads total - 16 stars on GitHub - 1 maintainer
Related Keywords
Software 195 GeneExpression 62 Clustering 61 Sequencing 52 ImmunoOncology 40 Microarray 35 RNASeq 33 SingleCell 32 Transcriptomics 31 Visualization 30 DifferentialExpression 30 MultipleComparison 25 Regression 24 FeatureExtraction 22 StatisticalMethod 22 Survival 18 Preprocessing 17 Proteomics 17 Network 16 Genetics 16 Normalization 15 GeneSetEnrichment 14 Pathways 14 DimensionReduction 14 DataImport 14 Annotation 13 QualityControl 13 BiomedicalInformatics 12 GraphAndNetwork 12 Microbiome 12 Transcription 12 SystemsBiology 12 FunctionalGenomics 11 Metagenomics 11 DataRepresentation 11 PrincipalComponent 11 SupportVectorMachine 10 Metabolomics 9 Epigenetics 9 Bayesian 9 MassSpectrometry 9 bioinformatics 9 bioconductor 8 GO 8 GenePrediction 8 r 8 Coverage 7 CellBiology 7 SNP 6 Pharmacogenomics 6 GeneticVariability 5 WholeGenome 5 HiddenMarkovModel 5 ChIPSeq 5 r-package 5 Lipidomics 5 BatchEffect 5 Pharmacogenetics 5 ShinyApps 5 GUI 5 NetworkInference 5 Alignment 5 DNASeq 5 Infrastructure 5 CellBasedAssays 4 GenomeWideAssociation 4 CopyNumberVariation 4 PeakDetection 4 GeneSignaling 4 NeuralNetwork 4 HiC 4 DecisionTree 4 FlowCytometry 4 DNAMethylation 4 rstats 4 DNA3DStructure 3 KEGG 3 mRNAMicroarray 3 bioconductor-package 3 Spatial 3 GenomeAnnotation 3 GeneRegulation 3 metagenomics 3 OneChannel 3 single-cell-rna-seq 3 ATACSeq 3 transcriptomics 3 GeneTarget 3 Technology 3 machine-learning 3 SomaticMutation 3 ExperimentalDesign 3 ddPCR 3 DifferentialPeakCalling 2 human-cell-atlas 2 multi-omics 2 ExperimentHubSoftware 2 GenomicVariation 2 miRNA 2 ComparativeGenomics 2