Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "Classification" keyword
RGSEA 1.36.0
Random Gene Set Enrichment Analysis3 versions - Latest release: 6 months ago - 17.3 thousand downloads total - 1 maintainer
microbiomeExplorer 1.12.0
Microbiome Exploration App3 versions - Latest release: 6 months ago - 6.29 thousand downloads total - 1 maintainer
Top 4.4% on bioconductor.org
4 versions - Latest release: 5 days ago - 5 dependent packages - 197 thousand downloads total - 162 stars on GitHub - 1 maintainer
SingleR 2.6.0
Reference-Based Single-Cell RNA-Seq Annotation4 versions - Latest release: 5 days ago - 5 dependent packages - 197 thousand downloads total - 162 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
3 versions - Latest release: 20 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: 20 days ago - 9 dependent packages - 226 thousand downloads total - 421 stars on GitHub - 1 maintainer
quantiseqr 1.10.0
Quantification of the Tumor Immune contexture from RNA-seq data3 versions - Latest release: 6 months ago - 2 dependent packages - 11.8 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 32.2 thousand downloads total - 2 maintainers
CRImage 1.50.0
CRImage a package to classify cells and calculate tumour cellularity3 versions - Latest release: 6 months ago - 32.2 thousand downloads total - 2 maintainers
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
graper 1.18.0
Adaptive penalization in high-dimensional regression and classification with external covariates ...3 versions - Latest release: 6 months ago - 5.5 thousand downloads total - 1 maintainer
SigCheck 2.34.0
Check a gene signature's prognostic performance against random signatures, known signatures, and ...3 versions - Latest release: 6 months ago - 14.4 thousand downloads total - 1 maintainer
switchBox 1.38.0
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair ...3 versions - Latest release: 6 months ago - 1 dependent package - 18.3 thousand downloads total - 3 maintainers
GGPA 1.14.0
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architec...3 versions - Latest release: 6 months ago - 4.23 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 8.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 1 maintainer
maigesPack 1.66.0
Functions to handle cDNA microarray data, including several methods of data analysis3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 1 maintainer
easier 1.8.0
Estimate Systems Immune Response from RNA-seq data3 versions - Latest release: 6 months ago - 4.36 thousand downloads total - 1 maintainer
epigenomix 1.42.0
Epigenetic and gene transcription data normalization and integration with mixture models3 versions - Latest release: 6 months ago - 20.6 thousand downloads total - 1 maintainer
rScudo 1.18.1
Signature-based Clustering for Diagnostic Purposes4 versions - Latest release: 3 months ago - 5.75 thousand downloads total - 3 stars on GitHub - 1 maintainer
LinkHD 1.16.0
LinkHD: a versatile framework to explore and integrate heterogeneous data3 versions - Latest release: 6 months ago - 4.84 thousand downloads total - 1 maintainer
geva 1.10.0
Gene Expression Variation Analysis (GEVA)3 versions - Latest release: 6 months ago - 2.79 thousand downloads total - 2 stars on GitHub - 1 maintainer
GARS 1.22.0
GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional...3 versions - Latest release: 6 months ago - 8.17 thousand downloads total - 1 maintainer
consensusOV 1.24.0
Gene expression-based subtype classification for high-grade serous ovarian cancer3 versions - Latest release: 6 months ago - 1 dependent package - 9.83 thousand downloads total - 1 maintainer
DeMixT 1.18.0
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components usin...3 versions - Latest release: 6 months ago - 7.82 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 27 thousand downloads total - 1 maintainer
Rmagpie 1.58.0
MicroArray Gene-expression-based Program In Error rate estimation3 versions - Latest release: 6 months ago - 27 thousand downloads total - 1 maintainer
TTMap 1.24.0
Two-Tier Mapper: a clustering tool based on topological data analysis3 versions - Latest release: 6 months ago - 6.96 thousand downloads total - 1 maintainer
omicade4 1.42.0
Multiple co-inertia analysis of omics datasets3 versions - Latest release: 6 months ago - 5 dependent packages - 24.7 thousand downloads total - 1 maintainer
katdetectr 1.4.0
Detection, Characterization and Visualization of Kataegis in Sequencing Data3 versions - Latest release: 6 months ago - 1.91 thousand downloads total - 1 maintainer
DaMiRseq 2.14.0
Data Mining for RNA-seq data: normalization, feature selection and classification3 versions - Latest release: 6 months ago - 1 dependent package - 13.6 thousand downloads total - 1 maintainer
idr2d 1.16.0
Irreproducible Discovery Rate for Genomic Interactions Data3 versions - Latest release: 6 months ago - 5.25 thousand downloads total - 1 maintainer
BadRegionFinder 1.30.0
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage3 versions - Latest release: 6 months ago - 11.5 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 28.9 thousand downloads total - 1 maintainer
iterativeBMA 1.60.0
The Iterative Bayesian Model Averaging (BMA) algorithm3 versions - Latest release: 6 months ago - 28.9 thousand downloads total - 1 maintainer
Top 6.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 48.3 thousand downloads total - 1 maintainer
CMA 1.60.0
Synthesis of microarray-based classification3 versions - Latest release: 6 months ago - 48.3 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 40.9 thousand downloads total - 1 maintainer
logicFS 2.22.0
Identification of SNP Interactions3 versions - Latest release: 6 months ago - 1 dependent package - 40.9 thousand downloads total - 1 maintainer
GPA 1.14.0
GPA (Genetic analysis incorporating Pleiotropy and Annotation)3 versions - Latest release: 6 months ago - 4.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
geNetClassifier 1.42.0
Classify diseases and build associated gene networks using gene expression profiles3 versions - Latest release: 6 months ago - 2 dependent packages - 26.2 thousand downloads total - 1 maintainer
CoreGx 2.6.1
Classes and Functions to Serve as the Basis for Other 'Gx' Packages4 versions - Latest release: 2 months ago - 5 dependent packages - 17.1 thousand downloads total - 1 maintainer
COSNet 1.36.0
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings3 versions - Latest release: 6 months ago - 14.6 thousand downloads total - 1 stars on GitHub
CAEN 1.10.0
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq3 versions - Latest release: 6 months ago - 2.78 thousand downloads total - 1 maintainer
a4Classif 1.50.0
Automated Affymetrix Array Analysis Classification Package3 versions - Latest release: 6 months ago - 1 dependent package - 37.5 thousand downloads total - 1 maintainer
scRepertoire 1.12.0
A toolkit for single-cell immune receptor profiling3 versions - Latest release: 6 months ago - 19.4 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
Top 8.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 30.8 thousand downloads total - 1 maintainer
MiPP 1.74.0
Misclassification Penalized Posterior Classification3 versions - Latest release: 6 months ago - 30.8 thousand downloads total - 1 maintainer
BioMM 1.18.0 removed
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using ...2 versions - Latest release: 6 months ago - 4.99 thousand downloads total - 1 maintainer
SIAMCAT 2.6.0
Statistical Inference of Associations between Microbial Communities And host phenoTypes3 versions - Latest release: 6 months ago - 11.8 thousand downloads total - 1 maintainer
sigFeature 1.20.0
sigFeature: Significant feature selection using SVM-RFE & t-statistic3 versions - Latest release: 6 months ago - 12.7 thousand downloads total - 1 maintainer
netDx 1.14.0
Network-based patient classifier3 versions - Latest release: 6 months ago - 4.36 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 32.2 thousand downloads total - 1 maintainer
gaga 2.48.0
GaGa hierarchical model for high-throughput data analysis3 versions - Latest release: 6 months ago - 1 dependent package - 32.2 thousand downloads total - 1 maintainer
rfPred 1.40.0
Assign rfPred functional prediction scores to a missense variants list3 versions - Latest release: 6 months ago - 17.4 thousand downloads total - 1 maintainer
Top 6.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 51.9 thousand downloads total - 1 maintainer
gpls 1.74.0
Classification using generalized partial least squares3 versions - Latest release: 6 months ago - 1 dependent package - 51.9 thousand downloads total - 1 maintainer
CytoDx 1.22.0
Robust prediction of clinical outcomes using cytometry data without cell gating3 versions - Latest release: 6 months ago - 7.94 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 2 dependent packages - 32.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
kebabs 1.36.0
Kernel-Based Analysis of Biological Sequences3 versions - Latest release: 6 months ago - 2 dependent packages - 32.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
Pigengene 1.28.0
Infers biological signatures from gene expression data3 versions - Latest release: 6 months ago - 1 dependent package - 13.6 thousand downloads total - 1 maintainer
messina 1.38.0
Single-gene classifiers and outlier-resistant detection of differential expression for two-group ...3 versions - Latest release: 6 months ago - 15.3 thousand downloads total - 1 maintainer
CNVPanelizer 1.34.0
Reliable CNV detection in targeted sequencing applications3 versions - Latest release: 6 months ago - 15.4 thousand downloads total - 1 maintainer
SCFA 1.12.0
SCFA: Subtyping via Consensus Factor Analysis3 versions - Latest release: 6 months ago - 3.45 thousand downloads total - 3 stars on GitHub - 1 maintainer
supersigs 1.10.0
Supervised mutational signatures3 versions - Latest release: 6 months ago - 2.71 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 9.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 29.4 thousand downloads total - 1 maintainer
procoil 2.30.0
Prediction of Oligomerization of Coiled Coil Proteins3 versions - Latest release: 6 months ago - 29.4 thousand downloads total - 1 maintainer
maPredictDSC 1.40.0
Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Dia...3 versions - Latest release: 6 months ago - 17.8 thousand downloads total - 1 maintainer
clstutils 1.50.0
Tools for performing taxonomic assignment3 versions - Latest release: 6 months ago - 23.1 thousand downloads total - 1 maintainer
KnowSeq 1.16.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline3 versions - Latest release: 6 months ago - 6.15 thousand downloads total - 1 maintainer
PAA 1.36.0
PAA (Protein Array Analyzer)3 versions - Latest release: 6 months ago - 17.6 thousand downloads total - 2 maintainers
LedPred 1.36.0
Learning from DNA to Predict Enhancers3 versions - Latest release: 6 months ago - 11.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 7.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 32.8 thousand downloads total - 1 maintainer
RBioinf 1.62.0
RBioinf3 versions - Latest release: 6 months ago - 32.8 thousand downloads total - 1 maintainer
GRridge 1.26.0 removed
Better prediction by use of co-data: Adaptive group-regularized ridge regression2 versions - Latest release: 6 months ago - 7.94 thousand downloads total - 1 maintainer
Top 6.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 33.7 thousand downloads total - 1 maintainer
vbmp 1.70.0
Variational Bayesian Multinomial Probit Regression3 versions - Latest release: 6 months ago - 33.7 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 45.9 thousand downloads total - 1 maintainer
AIMS 1.34.0
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype3 versions - Latest release: 6 months ago - 1 dependent package - 45.9 thousand downloads total - 1 maintainer
BUMHMM 1.26.0
Computational pipeline for computing probability of modification from structure probing experimen...3 versions - Latest release: 6 months ago - 9.56 thousand downloads total - 1 maintainer
ORFhunteR 1.10.0
Predict open reading frames in nucleotide sequences3 versions - Latest release: 6 months ago - 3.05 thousand downloads total - 1 stars on GitHub - 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
normr 1.28.0
Normalization and difference calling in ChIP-seq data3 versions - Latest release: 6 months ago - 15.7 thousand downloads total - 11 stars on GitHub - 1 maintainer
rRDP 1.36.0
Interface to the RDP Classifier3 versions - Latest release: 6 months ago - 14.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
cancerclass 1.46.0
Development and validation of diagnostic tests from high-dimensional molecular data3 versions - Latest release: 6 months ago - 22.7 thousand downloads total - 1 maintainer
bandle 1.6.0
An R package for the Bayesian analysis of differential subcellular localisation experiments3 versions - Latest release: 6 months ago - 2.26 thousand downloads total - 5 stars on GitHub - 1 maintainer
MAI 1.8.0
Mechanism-Aware Imputation3 versions - Latest release: 6 months ago - 2.68 thousand downloads total - 1 stars on GitHub - 1 maintainer
SemDist 1.36.0
Information Accretion-based Function Predictor Evaluation3 versions - Latest release: 6 months ago - 13.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
ggtreeDendro 1.4.0
Drawing 'dendrogram' using 'ggtree'3 versions - Latest release: 6 months ago - 1.94 thousand downloads total - 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
spatzie 1.8.0
Identification of enriched motif pairs from chromatin interaction data3 versions - Latest release: 6 months ago - 2.36 thousand downloads total - 1 maintainer
peco 1.14.0
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data3 versions - Latest release: 6 months ago - 4.1 thousand downloads total - 12 stars on GitHub - 1 maintainer
massiR 1.38.0
massiR: MicroArray Sample Sex Identifier3 versions - Latest release: 6 months ago - 16.5 thousand downloads total - 1 maintainer
Cepo 1.8.0
Cepo for the identification of differentially stable genes3 versions - Latest release: 6 months ago - 1 dependent package - 4.59 thousand downloads total - 1 maintainer
Clonality 1.50.0 removed
Clonality testing2 versions - Latest release: 6 months ago - 23.2 thousand downloads total - 1 maintainer
simpleSeg 1.6.0
A package to perform simple cell segmentation4 versions - Latest release: 13 days ago - 1.88 thousand downloads total - 0 stars on GitHub - 1 maintainer
PDATK 1.10.0
Pancreatic Ductal Adenocarcinoma Tool-Kit3 versions - Latest release: 6 months ago - 3.37 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
4 versions - Latest release: 4 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
EGSEA 1.30.1
Ensemble of Gene Set Enrichment Analyses4 versions - Latest release: 4 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
MEB 1.16.0
A normalization-invariant minimum enclosing ball method to detect differentially expressed genes ...3 versions - Latest release: 6 months ago - 4.67 thousand downloads total - 2 maintainers
Top 7.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 31.5 thousand downloads total - 1 maintainer
phenoTest 1.50.0
Tools to test association between gene expression and phenotype in a way that is efficient, struc...3 versions - Latest release: 6 months ago - 1 dependent package - 31.5 thousand downloads total - 1 maintainer
antiProfiles 1.42.0
Implementation of gene expression anti-profiles3 versions - Latest release: 6 months ago - 21.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
SingleCellSignalR 1.14.0
Cell Signalling Using Single Cell RNAseq Data Analysis3 versions - Latest release: 6 months ago - 3 dependent packages - 12 thousand downloads total - 1 maintainer
geneClassifiers 1.26.0
Application of gene classifiers3 versions - Latest release: 6 months ago - 8.67 thousand downloads total - 1 maintainer
biosigner 1.30.0
Signature discovery from omics data3 versions - Latest release: 6 months ago - 2 dependent packages - 14.2 thousand downloads total - 1 maintainer
MethPed 1.30.0
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes3 versions - Latest release: 6 months ago - 10.3 thousand downloads total - 1 maintainer
PROPS 1.24.0
PRObabilistic Pathway Score (PROPS)3 versions - Latest release: 6 months ago - 7.6 thousand downloads total - 1 maintainer
scds 1.18.0
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data3 versions - Latest release: 6 months ago - 2 dependent packages - 26.8 thousand downloads total - 1 maintainer
semisup 1.26.0
Semi-Supervised Mixture Model3 versions - Latest release: 6 months ago - 7.99 thousand downloads total - 1 stars on GitHub - 1 maintainer
TNBC.CMS 1.18.0
TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes3 versions - Latest release: 6 months ago - 5.19 thousand downloads total - 1 maintainer
miRNAtap 1.36.0
miRNAtap: microRNA Targets - Aggregated Predictions3 versions - Latest release: 6 months ago - 1 dependent package - 22.9 thousand downloads total - 1 maintainer
PoDCall 1.10.1
Positive Droplet Calling for DNA Methylation Droplet Digital PCR4 versions - Latest release: 4 months ago - 2.84 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
FCBF 2.10.0
Fast Correlation Based Filter for Feature Selection3 versions - Latest release: 6 months ago - 1 dependent package - 7.45 thousand downloads total - 1 maintainer
octad 1.4.0
Open Cancer TherApeutic Discovery (OCTAD)3 versions - Latest release: 6 months ago - 1.75 thousand downloads total - 1 maintainer
CONFESS 1.30.0
Cell OrderiNg by FluorEScence Signal3 versions - Latest release: 6 months ago - 10.9 thousand downloads total - 1 maintainer
a4Core 1.50.0
Automated Affymetrix Array Analysis Core Package3 versions - Latest release: 6 months ago - 3 dependent packages - 41.5 thousand downloads total - 1 maintainer
Related Keywords
Software
180
GeneExpression
57
Clustering
56
Sequencing
48
ImmunoOncology
38
Microarray
35
RNASeq
31
DifferentialExpression
29
SingleCell
29
Transcriptomics
27
Visualization
25
MultipleComparison
24
Regression
21
StatisticalMethod
19
FeatureExtraction
18
Survival
17
Network
17
Normalization
15
Genetics
15
Preprocessing
15
Proteomics
15
GeneSetEnrichment
13
DimensionReduction
13
SystemsBiology
12
Pathways
12
GraphAndNetwork
12
QualityControl
12
Microbiome
12
DataImport
12
Transcription
12
PrincipalComponent
10
SupportVectorMachine
10
BiomedicalInformatics
10
Metagenomics
10
DataRepresentation
10
FunctionalGenomics
10
Annotation
9
Epigenetics
9
MassSpectrometry
8
GenePrediction
8
GO
8
bioinformatics
8
Metabolomics
8
r
8
Bayesian
7
bioconductor
7
CellBiology
7
Pharmacogenomics
6
SNP
6
Coverage
6
Pharmacogenetics
5
GeneticVariability
5
GUI
5
NetworkInference
5
WholeGenome
5
DNASeq
5
Infrastructure
5
ChIPSeq
5
DNAMethylation
4
ShinyApps
4
FlowCytometry
4
Lipidomics
4
GeneSignaling
4
NeuralNetwork
4
DecisionTree
4
Alignment
4
HiC
4
HiddenMarkovModel
4
CopyNumberVariation
4
BatchEffect
4
rstats
4
r-package
4
clustering
3
bioconductor-package
3
KEGG
3
CellBasedAssays
3
OneChannel
3
Technology
3
GeneTarget
3
single-cell-rna-seq
3
machine-learning
3
ExperimentalDesign
3
SomaticMutation
3
GenomeWideAssociation
3
DNA3DStructure
3
GeneRegulation
3
PeakDetection
3
ATACSeq
3
mRNAMicroarray
3
GenomicVariation
2
miRNA
2
DifferentialMethylation
2
ddPCR
2
VariantAnnotation
2
NetworkEnrichment
2
human-cell-atlas
2
TimeCourse
2
Spatial
2
transcription-factors
2
GenomeAnnotation
2