bioconductor.org "BiomedicalInformatics" keyword
rScudo 1.28.0
Signature-based Clustering for Diagnostic Purposes8 versions - Latest release: 6 months ago - 25.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
ISAnalytics 1.22.0
Analyze gene therapy vector insertion sites data identified from genomics next generation sequenc...9 versions - Latest release: 6 months ago - 26.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
22 versions - Latest release: 3 months ago - 322 dependent packages - 8.76 million downloads total - 1 maintainer
limma 3.68.5
Linear Models for Microarray and Omics Data22 versions - Latest release: 3 months ago - 322 dependent packages - 8.76 million downloads total - 1 maintainer
Top 2.4% on bioconductor.org
8 versions - Latest release: 3 months ago - 2 dependent packages - 345 thousand downloads total - 1 maintainer
DiffBind 3.22.2
Differential Binding Analysis of ChIP-Seq Peak Data8 versions - Latest release: 3 months ago - 2 dependent packages - 345 thousand downloads total - 1 maintainer
Top 7.2% on bioconductor.org
9 versions - Latest release: 6 months ago - 1 dependent package - 60 thousand downloads total - 39 stars on GitHub - 1 maintainer
Rcpi 1.48.0
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery9 versions - Latest release: 6 months ago - 1 dependent package - 60 thousand downloads total - 39 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
7 versions - Latest release: 5 months ago - 1 dependent package - 96.3 thousand downloads total - 1 maintainer
flowAI 1.42.0
Automatic and interactive quality control for flow cytometry data7 versions - Latest release: 5 months ago - 1 dependent package - 96.3 thousand downloads total - 1 maintainer
CTDquerier 2.20.0
Package for CTDbase data query, visualization and downstream analysis7 versions - Latest release: 5 months ago - 30.1 thousand downloads total - 1 maintainer
faers 1.8.0
R interface for FDA Adverse Event Reporting System6 versions - Latest release: 5 months ago - 18 thousand downloads total - 54 stars on GitHub - 1 maintainer
immunotation 1.20.0
Tools for working with diverse immune genes8 versions - Latest release: 6 months ago - 20.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
TRONCO 2.44.0
TRONCO, an R package for TRanslational ONCOlogy8 versions - Latest release: 6 months ago - 43.3 thousand downloads total - 1 maintainer
ClustIRR 1.10.0
Clustering of Immune Receptor Repertoires6 versions - Latest release: 6 months ago - 16.2 thousand downloads total - 6 stars on GitHub - 1 maintainer
OMICsPCA 1.30.0
An R package for quantitative integration and analysis of multiple omics assays from heterogeneou...7 versions - Latest release: 6 months ago - 33.1 thousand downloads total - 1 maintainer
EWCE 1.20.0
Expression Weighted Celltype Enrichment9 versions - Latest release: 5 months ago - 38.7 thousand downloads total - 60 stars on GitHub - 1 maintainer
mdp 1.32.0
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their ...7 versions - Latest release: 6 months ago - 28.6 thousand downloads total - 1 maintainer
hummingbird 1.22.0
Bayesian Hidden Markov Model for the detection of differentially methylated regions4 versions - Latest release: 3 months ago - 20.6 thousand downloads total - 1 maintainer
metaseqR2 1.24.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...9 versions - Latest release: 5 months ago - 29.6 thousand downloads total - 1 maintainer
miRspongeR 2.16.2
Identification and analysis of miRNA sponge regulation10 versions - Latest release: about 1 month ago - 1 dependent package - 27 thousand downloads total - 6 stars on GitHub - 1 maintainer
RImmPort 1.40.0
RImmPort: Enabling Ready-for-analysis Immunology Research Data7 versions - Latest release: 5 months ago - 25.9 thousand downloads total - 2 maintainers
rmelting 1.28.0
R Interface to MELTING 57 versions - Latest release: 5 months ago - 22.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
ZygosityPredictor 1.12.0
Package for prediction of zygosity for variants/genes in NGS data7 versions - Latest release: 6 months ago - 15.7 thousand downloads total - 1 maintainer
betaHMM 1.8.0
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Be...7 versions - Latest release: 6 months ago - 15.7 thousand downloads total - 1 maintainer
miRSM 2.8.2
Inferring miRNA sponge modules in heterogeneous data9 versions - Latest release: about 2 months ago - 28.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
cbaf 1.34.0
Automated functions for comparing various omic data from cbioportal.org8 versions - Latest release: 6 months ago - 28.5 thousand downloads total - 1 maintainer
timescape 1.36.0
Patient Clonal Timescapes7 versions - Latest release: 6 months ago - 25.5 thousand downloads total - 1 maintainer
microSTASIS 1.12.0
Microbiota STability ASsessment via Iterative cluStering7 versions - Latest release: 6 months ago - 7.86 thousand downloads total - 1 maintainer
Top 0.6% on bioconductor.org
31 versions - Latest release: 16 days ago - 181 dependent packages - 4.8 million downloads total - 4 maintainers
edgeR 4.10.6
Empirical Analysis of Digital Gene Expression Data in R31 versions - Latest release: 16 days ago - 181 dependent packages - 4.8 million downloads total - 4 maintainers
ASAFE 1.38.0
Ancestry Specific Allele Frequency Estimation7 versions - Latest release: 6 months ago - 25.4 thousand downloads total - 1 maintainer
islify 1.4.0
Automatic scoring and classification of cell-based assay images3 versions - Latest release: 6 months ago - 9.74 thousand downloads total - 1 maintainer
SPIAT 1.14.0
Spatial Image Analysis of Tissues12 versions - Latest release: 6 months ago - 23.9 thousand downloads total - 30 stars on GitHub - 1 maintainer
OncoScore 1.40.0
A tool to identify potentially oncogenic genes7 versions - Latest release: 6 months ago - 29.4 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
7 versions - Latest release: 5 months ago - 1 dependent package - 83.8 thousand downloads total - 6 stars on GitHub - 1 maintainer
fmcsR 1.54.0
Mismatch Tolerant Maximum Common Substructure Searching7 versions - Latest release: 5 months ago - 1 dependent package - 83.8 thousand downloads total - 6 stars on GitHub - 1 maintainer
ssPATHS 1.26.0
ssPATHS: Single Sample PATHway Score7 versions - Latest release: 6 months ago - 1 maintainer
GAprediction 1.38.0
Prediction of gestational age with Illumina HumanMethylation450 data7 versions - Latest release: 6 months ago - 23.3 thousand downloads total - 1 maintainer
MEAT 1.24.0
Muscle Epigenetic Age Test7 versions - Latest release: 5 months ago - 25.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
MouseFM 1.22.0
In-silico methods for genetic finemapping in inbred mice9 versions - Latest release: 5 months ago - 22.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
notameStats 1.2.0
Workflow for non-targeted LC-MS metabolic profiling2 versions - Latest release: 6 months ago - 3.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
notameViz 1.2.0
Workflow for non-targeted LC-MS metabolic profiling3 versions - Latest release: 5 months ago - 4.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
notame 1.2.0
Workflow for non-targeted LC-MS metabolic profiling3 versions - Latest release: 6 months ago - 5.73 thousand downloads total - 6 stars on GitHub - 1 maintainer
batchCorr 1.2.0
Within And Between Batch Correction Of LC-MS Metabolomics Data2 versions - Latest release: 6 months ago - 4.79 thousand downloads total - 0 stars on GitHub - 1 maintainer
IsoformSwitchAnalyzeR 2.12.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...7 versions - Latest release: 5 months ago - 65.3 thousand downloads total - 1 maintainer
OPWeight 1.34.0
Optimal p-value weighting with independent information7 versions - Latest release: 6 months ago - 28.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
netboost 2.20.0
Network Analysis Supported by Boosting8 versions - Latest release: 6 months ago - 16.5 thousand downloads total - 1 maintainer
fobitools 1.20.0
Tools for Manipulating the FOBI Ontology7 versions - Latest release: 5 months ago - 14.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
cfTools 1.12.0
Informatics Tools for Cell-Free DNA Study7 versions - Latest release: 5 months ago - 8.79 thousand downloads total - 11 stars on GitHub - 1 maintainer
psichomics 1.38.1
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation10 versions - Latest release: 5 months ago - 30 thousand downloads total - 37 stars on GitHub - 1 maintainer
IgGeneUsage 1.26.0
Differential gene usage in immune repertoires7 versions - Latest release: 5 months ago - 16.2 thousand downloads total - 6 stars on GitHub - 1 maintainer
frenchFISH 1.24.0
Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections7 versions - Latest release: 5 months ago - 12.9 thousand downloads total - 1 maintainer
decompTumor2Sig 2.28.1
Decomposition of individual tumors into mutational signatures by signature refitting8 versions - Latest release: 3 months ago - 1 dependent package - 23.8 thousand downloads total - 1 maintainer
artMS 1.29.0
Analytical R tools for Mass Spectrometry7 versions - Latest release: 6 months ago - 22 thousand downloads total - 1 maintainer
Top 6.3% on bioconductor.org
7 versions - Latest release: 6 months ago - 8 dependent packages - 543 thousand downloads total - 17 stars on GitHub - 1 maintainer
ChemmineR 3.64.0
Cheminformatics Toolkit for R7 versions - Latest release: 6 months ago - 8 dependent packages - 543 thousand downloads total - 17 stars on GitHub - 1 maintainer
pfamAnalyzeR 1.12.0
Identification of domain isotypes in pfam data7 versions - Latest release: 5 months ago - 1 dependent package - 21.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
mistyR 1.20.0
Multiview Intercellular SpaTial modeling framework8 versions - Latest release: 5 months ago - 19 thousand downloads total - 74 stars on GitHub - 1 maintainer
gwasurvivr 1.30.0
gwasurvivr: an R package for genome wide survival analysis7 versions - Latest release: 6 months ago - 23.2 thousand downloads total - 13 stars on GitHub - 1 maintainer
MOGAMUN 1.22.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks7 versions - Latest release: 5 months ago - 13.9 thousand downloads total - 13 stars on GitHub - 1 maintainer
roastgsa 1.10.0
Rotation based gene set analysis6 versions - Latest release: 5 months ago - 11.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
ELViS 1.4.0
An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Rea...3 versions - Latest release: 6 months ago - 7.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
spaSim 1.14.0
Spatial point data simulator for tissue images7 versions - Latest release: 5 months ago - 12.7 thousand downloads total - 2 stars on GitHub - 1 maintainer
TENET 1.4.0
R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key...4 versions - Latest release: 6 months ago - 6.98 thousand downloads total - 2 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.26.0 removed
Random walk with restart on multiplex and heterogeneous Networks4 versions - Latest release: almost 2 years ago - 1 dependent package - 10.7 thousand downloads total - 23 stars on GitHub - 1 maintainer
eiR 1.52.0
Accelerated similarity searching of small molecules7 versions - Latest release: 5 months ago - 28.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
GRaNIE 1.16.0
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...7 versions - Latest release: 6 months ago - 20.5 thousand downloads total - 1 maintainer
GenomicOZone 1.26.0
Delineate outstanding genomic zones of differential gene activity7 versions - Latest release: 6 months ago - 18.7 thousand downloads total - 1 maintainer
randRotation 1.23.0
Random Rotation Methods for High Dimensional Data with Batch Structure7 versions - Latest release: 5 months ago - 12.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
powerTCR 1.32.0
Model-Based Comparative Analysis of the TCR Repertoire7 versions - Latest release: 6 months ago - 1 dependent package - 49.6 thousand downloads total - 1 maintainer
SigsPack 1.26.0
Mutational Signature Estimation for Single Samples7 versions - Latest release: 6 months ago - 17.6 thousand downloads total - 2 stars on GitHub - 1 maintainer
LACE 2.16.0
Longitudinal Analysis of Cancer Evolution (LACE)8 versions - Latest release: 6 months ago - 18.6 thousand downloads total - 16 stars on GitHub - 1 maintainer
SparseSignatures 2.22.0
SparseSignatures7 versions - Latest release: 6 months ago - 22 thousand downloads total - 11 stars on GitHub - 1 maintainer
SiPSiC 1.12.0
Calculate Pathway Scores for Each Cell in scRNA-Seq Data11 versions - Latest release: 6 months ago - 10.1 thousand downloads total - 1 maintainer
gCrisprTools 2.18.0
Suite of Functions for Pooled Crispr Screen QC and Analysis7 versions - Latest release: 5 months ago - 27.4 thousand downloads total - 1 maintainer
dearseq 1.24.0
Differential Expression Analysis for RNA-seq data through a robust variance component test7 versions - Latest release: 5 months ago - 2 dependent packages - 26.7 thousand downloads total - 6 stars on GitHub - 1 maintainer
RESOLVE 1.14.0
RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes7 versions - Latest release: 5 months ago - 11.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
sitadela 1.20.0
An R package for the easy provision of simple but complete tab-delimited genomic annotation from ...7 versions - Latest release: 6 months ago - 14.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
VERSO 1.22.0
Viral Evolution ReconStructiOn (VERSO)7 versions - Latest release: 6 months ago - 13.3 thousand downloads total - 7 stars on GitHub - 1 maintainer
rexposome 1.34.2
Exposome exploration and outcome data analysis8 versions - Latest release: 6 months ago - 1 dependent package - 28.1 thousand downloads total - 1 maintainer
drugTargetInteractions 1.20.0
Drug-Target Interactions7 versions - Latest release: 6 months ago - 14.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
RIVER 1.36.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)7 versions - Latest release: 5 months ago - 21.9 thousand downloads total - 12 stars on GitHub - 1 maintainer
signifinder 1.13.0
Collection and implementation of public transcriptional cancer signatures8 versions - Latest release: 6 months ago - 10.9 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 3.0% on bioconductor.org
7 versions - Latest release: 6 months ago - 2 dependent packages - 248 thousand downloads total - 10 stars on GitHub - 1 maintainer
ChemmineOB 1.50.0
R interface to a subset of OpenBabel functionalities7 versions - Latest release: 6 months ago - 2 dependent packages - 248 thousand downloads total - 10 stars on GitHub - 1 maintainer
protGear 1.16.0
Protein Micro Array Data Management and Interactive Visualization7 versions - Latest release: 6 months ago - 15.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
simona 1.10.0
Semantic Similarity on Bio-Ontologies9 versions - Latest release: 6 months ago - 30.6 thousand downloads total - 18 stars on GitHub - 1 maintainer
messina 1.48.0
Single-gene classifiers and outlier-resistant detection of differential expression for two-group ...7 versions - Latest release: 5 months ago - 34.7 thousand downloads total - 1 maintainer
easier 1.18.0
Estimate Systems Immune Response from RNA-seq data7 versions - Latest release: 6 months ago - 22.9 thousand downloads total - 1 maintainer
iNETgrate 1.10.0
Integrates DNA methylation data with gene expression in a single gene network7 versions - Latest release: 6 months ago - 16.1 thousand downloads total - 65 stars on GitHub - 1 maintainer
PhenoGeneRanker 1.20.0
PhenoGeneRanker: A gene and phenotype prioritization tool7 versions - Latest release: 5 months ago - 13.2 thousand downloads total - 1 maintainer
geneClassifiers 1.36.0
Application of gene classifiers7 versions - Latest release: 6 months ago - 26.8 thousand downloads total - 1 maintainer
Pigengene 1.38.0
Infers biological signatures from gene expression data8 versions - Latest release: 5 months ago - 1 dependent package - 35.5 thousand downloads total - 1 maintainer
proteasy 1.6.0 removed
Protease Mapping3 versions - Latest release: over 2 years ago - 1.34 thousand downloads total - 2 stars on GitHub - 1 maintainer
GeneAccord 1.18.0 removed
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients1 version - Latest release: about 3 years ago - 4.41 thousand downloads total - 2 stars on GitHub - 1 maintainer
sincell 1.44.0
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data7 versions - Latest release: 6 months ago - 35 thousand downloads total - 1 maintainer
oppti 1.24.0 removed
Outlier Protein and Phosphosite Target Identifier6 versions - Latest release: 11 months ago - 8.98 thousand downloads total - 2 stars on GitHub - 1 maintainer
netDx 1.20.0 removed
Network-based patient classifier5 versions - Latest release: over 1 year ago - 6.47 thousand downloads total - 1 maintainer
coRdon 1.30.0
Codon Usage Analysis and Prediction of Gene Expressivity7 versions - Latest release: 6 months ago - 34.2 thousand downloads total - 22 stars on GitHub - 1 maintainer
deco 1.18.0 removed
Decomposing Heterogeneous Cohorts using Omic Data Profiling2 versions - Latest release: almost 3 years ago - 4.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
psygenet2r 1.37.1 removed
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric...5 versions - Latest release: almost 2 years ago - 14.3 thousand downloads total - 1 maintainer
CancerInSilico 2.24.0 removed
An R interface for computational modeling of tumor progression3 versions - Latest release: over 2 years ago - 9.16 thousand downloads total - 2 maintainers
STROMA4 1.26.0 removed
Assign Properties to TNBC Patients3 versions - Latest release: almost 3 years ago - 8.43 thousand downloads total - 1 maintainer
Related Keywords
Software
96
GeneExpression
31
Clustering
28
SystemsBiology
28
ImmunoOncology
28
RNASeq
25
DataImport
23
Visualization
22
Transcriptomics
22
Sequencing
21
DifferentialExpression
21
Genetics
20
MultipleComparison
20
FunctionalGenomics
19
Transcription
18
Regression
17
Normalization
17
GeneSetEnrichment
16
Microarray
16
Proteomics
16
CellBiology
16
SingleCell
13
Epigenetics
13
QualityControl
13
Metabolomics
13
Classification
12
Pathways
11
BatchEffect
11
Bayesian
11
GraphAndNetwork
11
Preprocessing
11
Network
11
Cheminformatics
10
SomaticMutation
10
DNAMethylation
9
Survival
8
Pharmacogenomics
8
AlternativeSplicing
8
GenePrediction
8
SNP
7
Infrastructure
7
DifferentialMethylation
7
Annotation
7
MathematicalBiology
6
GeneTarget
6
Spatial
6
NetworkInference
6
GeneRegulation
6
Pharmacogenetics
6
GenomicVariation
6
DifferentialSplicing
6
MassSpectrometry
6
DataRepresentation
6
ChIPSeq
5
mRNAMicroarray
5
TimeCourse
5
r
5
FunctionalPrediction
5
CellBasedAssays
5
KEGG
5
GeneticVariability
5
FeatureExtraction
5
StatisticalMethod
5
DimensionReduction
5
bioinformatics
4
MicrotitrePlateAssay
4
MicroRNAArray
4
OneChannel
4
Coverage
4
PrincipalComponent
4
TranscriptomeVariant
3
BiologicalQuestion
3
ExperimentalDesign
3
ExonArray
3
GO
3
ProprietaryPlatforms
3
DNASeq
3
ReportWriting
3
bioconductor
3
ATACSeq
3
MethylSeq
3
MethylationArray
3
HiddenMarkovModel
3
immunoinformatics
2
GenomeWideAssociation
2
b-cell-receptor
2
mirna
2
cerna
2
WorkflowStep
2
immunology
2
clustering
2
VariantAnnotation
2
r-package
2
HistoneModification
2
PatternLogic
2
transcriptomics
2
TwoChannel
2
CopyNumberVariation
2
GUI
2
differential-gene-expression
2