bioconductor.org "SystemsBiology" keyword
SETA 1.2.0
Single Cell Ecological Taxonomic Analysis2 versions - Latest release: 6 months ago - 9.97 thousand downloads total - 1 maintainer
XINA 1.30.0
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis7 versions - Latest release: 6 months ago - 26.1 thousand downloads total - 1 maintainer
genomicInstability 1.18.0
Genomic Instability estimation for scRNA-Seq7 versions - Latest release: 6 months ago - 19.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
ReactomeGSA 1.26.0
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis9 versions - Latest release: 6 months ago - 38.1 thousand downloads total - 33 stars on GitHub - 1 maintainer
cogena 1.46.0
co-expressed gene-set enrichment analysis7 versions - Latest release: 6 months ago - 47.6 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
32 versions - Latest release: 2 days ago - 181 dependent packages - 4.96 million downloads total - 4 maintainers
edgeR 4.10.7
Empirical Analysis of Digital Gene Expression Data in R32 versions - Latest release: 2 days ago - 181 dependent packages - 4.96 million downloads total - 4 maintainers
Top 6.4% on bioconductor.org
7 versions - Latest release: 6 months ago - 3 dependent packages - 104 thousand downloads total - 1 maintainer
hpar 1.54.0
Human Protein Atlas in R7 versions - Latest release: 6 months ago - 3 dependent packages - 104 thousand downloads total - 1 maintainer
MEIGOR 1.46.0
MEIGOR - MEtaheuristics for bIoinformatics Global Optimization9 versions - Latest release: 6 months ago - 2 dependent packages - 38.6 thousand downloads total - 1 maintainer
TreeAndLeaf 1.24.0
Displaying binary trees with focus on dendrogram leaves8 versions - Latest release: 6 months ago - 1 dependent package - 31.7 thousand downloads total - 15 stars on GitHub - 1 maintainer
MouseFM 1.22.0
In-silico methods for genetic finemapping in inbred mice9 versions - Latest release: 6 months ago - 24.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
MetaProViz 4.0.0
METabolomics pre-PRocessing, functiOnal analysis and VIZualisation1 version - Latest release: 7 months ago - 8.02 thousand downloads total - 26 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
22 versions - Latest release: 3 months ago - 322 dependent packages - 9.06 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 - 9.06 million downloads total - 1 maintainer
IsoformSwitchAnalyzeR 2.12.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...7 versions - Latest release: 6 months ago - 76 thousand downloads total - 137 stars on GitHub - 1 maintainer
GenomicSuperSignature 1.20.0
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases8 versions - Latest release: 6 months ago - 29.3 thousand downloads total - 16 stars on GitHub - 1 maintainer
easier 1.18.0
Estimate Systems Immune Response from RNA-seq data7 versions - Latest release: 6 months ago - 25.4 thousand downloads total - 1 maintainer
PhenoGeneRanker 1.20.0
PhenoGeneRanker: A gene and phenotype prioritization tool7 versions - Latest release: 5 months ago - 14.2 thousand downloads total - 1 maintainer
KBoost 1.20.0
Inference of gene regulatory networks from gene expression data7 versions - Latest release: 5 months ago - 15.4 thousand downloads total - 4 stars on GitHub - 1 maintainer
epiNEM 1.36.0
epiNEM7 versions - Latest release: 6 months ago - 4 dependent packages - 35.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
INSPEcT 1.42.0
Modeling RNA synthesis, processing and degradation with RNA-seq data8 versions - Latest release: 6 months ago - 48.5 thousand downloads total - 2 maintainers
Top 3.0% on bioconductor.org
7 versions - Latest release: 6 months ago - 4 dependent packages - 262 thousand downloads total - 6 stars on GitHub - 1 maintainer
gage 2.62.0
Generally Applicable Gene-set Enrichment for Pathway Analysis7 versions - Latest release: 6 months ago - 4 dependent packages - 262 thousand downloads total - 6 stars on GitHub - 1 maintainer
DeMAND 1.42.0
DeMAND7 versions - Latest release: 6 months ago - 27 thousand downloads total - 2 maintainers
MWASTools 1.36.0
MWASTools: an integrated pipeline to perform metabolome-wide association studies7 versions - Latest release: 6 months ago - 1 dependent package - 39.6 thousand downloads total - 2 maintainers
epidecodeR 1.20.0
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation7 versions - Latest release: 6 months ago - 20.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
CHRONOS 1.40.0
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis7 versions - Latest release: 6 months ago - 31.3 thousand downloads total - 1 maintainer
pmm 1.44.0
Parallel Mixed Model7 versions - Latest release: 6 months ago - 27 thousand downloads total - 1 maintainer
rain 1.46.0
Rhythmicity Analysis Incorporating Non-parametric Methods7 versions - Latest release: 6 months ago - 43.9 thousand downloads total - 1 maintainer
SPONGE 1.34.1
Sparse Partial Correlations On Gene Expression9 versions - Latest release: 5 months ago - 2 dependent packages - 40.9 thousand downloads total - 1 maintainer
artMS 1.29.0
Analytical R tools for Mass Spectrometry7 versions - Latest release: 6 months ago - 31.2 thousand downloads total - 14 stars on GitHub - 1 maintainer
SMITE 1.40.0
Significance-based Modules Integrating the Transcriptome and Epigenome7 versions - Latest release: 6 months ago - 38.2 thousand downloads total - 1 stars on GitHub - 2 maintainers
mnem 1.28.0
Mixture Nested Effects Models7 versions - Latest release: 5 months ago - 4 dependent packages - 33.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
nempi 1.20.0
Inferring unobserved perturbations from gene expression data7 versions - Latest release: 6 months ago - 19.5 thousand downloads total - 2 stars on GitHub - 1 maintainer
protGear 1.16.0
Protein Micro Array Data Management and Interactive Visualization7 versions - Latest release: 6 months ago - 23.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
GenomicOZone 1.26.0
Delineate outstanding genomic zones of differential gene activity7 versions - Latest release: 6 months ago - 25.3 thousand downloads total - 1 maintainer
PrInCE 1.28.0
Predicting Interactomes from Co-Elution7 versions - Latest release: 6 months ago - 26.1 thousand downloads total - 8 stars on GitHub - 1 maintainer
mistyR 1.20.0
Multiview Intercellular SpaTial modeling framework8 versions - Latest release: 5 months ago - 24.4 thousand downloads total - 74 stars on GitHub - 1 maintainer
vulcan 1.34.0
VirtUaL ChIP-Seq data Analysis using Networks7 versions - Latest release: 6 months ago - 28.3 thousand downloads total - 1 maintainer
doseR 1.28.0
doseR7 versions - Latest release: 6 months ago - 26.8 thousand downloads total - 1 maintainer
Top 7.2% on bioconductor.org
9 versions - Latest release: 6 months ago - 1 dependent package - 60.5 thousand downloads total - 40 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 - 60.5 thousand downloads total - 40 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
7 versions - Latest release: 6 months ago - 7 dependent packages - 131 thousand downloads total - 1 maintainer
viper 1.46.0
Virtual Inference of Protein-activity by Enriched Regulon analysis7 versions - Latest release: 6 months ago - 7 dependent packages - 131 thousand downloads total - 1 maintainer
regutools 1.24.0
regutools: an R package for data extraction from RegulonDB7 versions - Latest release: 6 months ago - 24.8 thousand downloads total - 5 stars on GitHub - 1 maintainer
ceRNAnetsim 1.24.0
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)8 versions - Latest release: 6 months ago - 21.4 thousand downloads total - 5 stars on GitHub - 1 maintainer
wppi 1.20.0
Weighting protein-protein interactions9 versions - Latest release: 5 days ago - 18.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
dearseq 1.24.0
Differential Expression Analysis for RNA-seq data through a robust variance component test7 versions - Latest release: 6 months ago - 2 dependent packages - 33.3 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
7 versions - Latest release: 6 months ago - 9 dependent packages - 765 thousand downloads total - 52 stars on GitHub - 1 maintainer
pathview 1.52.0
a tool set for pathway based data integration and visualization7 versions - Latest release: 6 months ago - 9 dependent packages - 765 thousand downloads total - 52 stars on GitHub - 1 maintainer
dominoSignal 1.6.0
Cell Communication Analysis for Single Cell RNA Sequencing5 versions - Latest release: 6 months ago - 14.6 thousand downloads total - 8 stars on GitHub - 1 maintainer
bnem 1.20.0
Training of logical models from indirect measurements of perturbation experiments7 versions - Latest release: 6 months ago - 22.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
roastgsa 1.10.0
Rotation based gene set analysis6 versions - Latest release: 6 months ago - 16.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
ExpoRiskR 1.0.0
Exposure-Aware Multi-Omics Risk Modeling1 version - Latest release: 7 months ago - 6.49 thousand downloads total - 0 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 - 19.4 thousand downloads total - 13 stars on GitHub - 1 maintainer
progeny 1.34.0
Pathway RespOnsive GENes for activity inference from gene expression7 versions - Latest release: 5 months ago - 2 dependent packages - 85.7 thousand downloads total - 130 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
7 versions - Latest release: 7 months ago - 2 dependent packages - 274 thousand downloads total - 319 stars on GitHub - 1 maintainer
microbiome 1.34.0
Microbiome Analytics7 versions - Latest release: 7 months ago - 2 dependent packages - 274 thousand downloads total - 319 stars on GitHub - 1 maintainer
CCPlotR 1.10.0
Plots For Visualising Cell-Cell Interactions6 versions - Latest release: 6 months ago - 16.7 thousand downloads total - 47 stars on GitHub - 1 maintainer
iNETgrate 1.10.0
Integrates DNA methylation data with gene expression in a single gene network7 versions - Latest release: 6 months ago - 18.1 thousand downloads total - 79 stars on GitHub - 1 maintainer
seqArchR 1.14.0 removed
Identify Different Architectures of Sequence Elements6 versions - Latest release: 12 months ago - 1 dependent package - 8.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
geneplast 1.38.0
Evolutionary and plasticity analysis of orthologous groups7 versions - Latest release: 6 months ago - 1 dependent package - 36.9 thousand downloads total - 1 maintainer
RIVER 1.36.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)7 versions - Latest release: 6 months ago - 30.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
Pigengene 1.38.0
Infers biological signatures from gene expression data8 versions - Latest release: 6 months ago - 1 dependent package - 39.4 thousand downloads total - 1 maintainer
MIRit 1.8.0
Integrate microRNA and gene expression to decipher pathway complexity10 versions - Latest release: 6 months ago - 17.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
scQTLtools 1.4.0
scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of singl...7 versions - Latest release: 6 months ago - 13.3 thousand downloads total - 7 stars on GitHub - 1 maintainer
SGCP 1.12.0
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...11 versions - Latest release: 10 days ago - 13.6 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 - 39 thousand downloads total - 1 maintainer
geva 1.20.0
Gene Expression Variation Analysis (GEVA)7 versions - Latest release: 5 months ago - 20.3 thousand downloads total - 2 stars on GitHub - 1 maintainer
BioNERO 1.20.0
Biological Network Reconstruction Omnibus10 versions - Latest release: 6 months ago - 1 dependent package - 40.4 thousand downloads total - 38 stars on GitHub - 1 maintainer
COTAN 2.12.1
COexpression Tables ANalysis24 versions - Latest release: 4 months ago - 24.5 thousand downloads total - 17 stars on GitHub - 1 maintainer
cytoMEM 1.16.0
Marker Enrichment Modeling (MEM)7 versions - Latest release: 4 months ago - 19.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
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
diggit 1.44.0
Inference of Genetic Variants Driving Cellular Phenotypes7 versions - Latest release: 5 months ago - 32.9 thousand downloads total - 1 maintainer
pathwayPCA 1.28.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection7 versions - Latest release: 6 months ago - 1 dependent package - 29.3 thousand downloads total - 11 stars on GitHub - 1 maintainer
syntenet 1.14.0
Inference And Analysis Of Synteny Networks11 versions - Latest release: 5 months ago - 1 dependent package - 24.4 thousand downloads total - 43 stars on GitHub - 1 maintainer
OmnipathR 4.0.0
OmniPath web service client and more13 versions - Latest release: 5 months ago - 3 dependent packages - 106 thousand downloads total - 175 stars on GitHub - 1 maintainer
DEsubs 1.38.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...7 versions - Latest release: 6 months ago - 36.9 thousand downloads total - 2 maintainers
MOMA 1.24.0
Multi Omic Master Regulator Analysis7 versions - Latest release: 6 months ago - 27.6 thousand downloads total - 6 stars on GitHub - 1 maintainer
BioCor 1.36.0
Functional Similarities7 versions - Latest release: 6 months ago - 36.2 thousand downloads total - 14 stars on GitHub - 1 maintainer
rcellminer 2.34.0
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines8 versions - Latest release: 5 months ago - 43.1 thousand downloads total - 3 maintainers
oppar 1.40.0
Outlier profile and pathway analysis in R8 versions - Latest release: 6 months ago - 36.6 thousand downloads total - 1 maintainer
CausalR 1.44.0
Causal network analysis methods7 versions - Latest release: 6 months ago - 32.6 thousand downloads total - 2 maintainers
Top 4.5% on bioconductor.org
7 versions - Latest release: 6 months ago - 2 dependent packages - 160 thousand downloads total - 1 maintainer
GENIE3 1.34.0
GEne Network Inference with Ensemble of trees7 versions - Latest release: 6 months ago - 2 dependent packages - 160 thousand downloads total - 1 maintainer
IMMAN 1.32.0
Interlog protein network reconstruction by Mapping and Mining ANalysis7 versions - Latest release: 6 months ago - 23.8 thousand downloads total - 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
MIRA 1.34.0
Methylation-Based Inference of Regulatory Activity7 versions - Latest release: 6 months ago - 1 dependent package - 34.8 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: 6 months ago - 29.6 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
10 versions - Latest release: 3 months ago - 4 dependent packages - 88 thousand downloads total - 1 maintainer
RedeR 3.8.1
Interactive visualization and manipulation of nested networks10 versions - Latest release: 3 months ago - 4 dependent packages - 88 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
8 versions - Latest release: 6 months ago - 1 dependent package - 58.5 thousand downloads total - 1 maintainer
EGSEA 1.40.0
Ensemble of Gene Set Enrichment Analyses8 versions - Latest release: 6 months ago - 1 dependent package - 58.5 thousand downloads total - 1 maintainer
KnowSeq 1.25.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline7 versions - Latest release: 6 months ago - 27.5 thousand downloads total - 1 maintainer
GmicR 1.26.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...7 versions - Latest release: 6 months ago - 23.9 thousand downloads total - 1 maintainer
COCOA 2.26.0
Coordinate Covariation Analysis7 versions - Latest release: 6 months ago - 29.5 thousand downloads total - 1 maintainer
Top 3.1% on bioconductor.org
7 versions - Latest release: 6 months ago - 4 dependent packages - 141 thousand downloads total - 1 maintainer
RankProd 3.38.0
Rank Product method for identifying differentially expressed genes with application in meta-analysis7 versions - Latest release: 6 months ago - 4 dependent packages - 141 thousand downloads total - 1 maintainer
EGAD 1.40.0
Extending guilt by association by degree7 versions - Latest release: 6 months ago - 26.2 thousand downloads total - 1 maintainer
transcriptogramer 1.34.0
Transcriptional analysis based on transcriptograms7 versions - Latest release: 5 months ago - 23.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
pfamAnalyzeR 1.12.0
Identification of domain isotypes in pfam data7 versions - Latest release: 6 months ago - 1 dependent package - 21.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
Path2PPI 1.42.0
Prediction of pathway-related protein-protein interaction networks7 versions - Latest release: 6 months ago - 26.4 thousand downloads total - 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
LOLA 1.42.0
Locus overlap analysis for enrichment of genomic ranges8 versions - Latest release: 6 months ago - 5 dependent packages - 1 maintainer
sRACIPE 2.4.0
Systems biology tool to simulate gene regulatory circuits8 versions - Latest release: 6 months ago - 18.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
gCrisprTools 2.18.0
Suite of Functions for Pooled Crispr Screen QC and Analysis7 versions - Latest release: 6 months ago - 27.4 thousand downloads total - 1 maintainer
rsemmed 1.22.0
An interface to the Semantic MEDLINE database7 versions - Latest release: 6 months ago - 14.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
magrene 1.14.0
Motif Analysis In Gene Regulatory Networks7 versions - Latest release: 6 months ago - 11.8 thousand downloads total - 3 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
HPiP 1.18.0
Host-Pathogen Interaction Prediction9 versions - Latest release: 6 months ago - 13.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
DeProViR 1.4.0 removed
A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Prot...4 versions - Latest release: over 1 year ago - 1.83 thousand downloads total - 2 stars on GitHub - 1 maintainer
Related Keywords
Software
115
GeneExpression
58
Network
47
Pathways
33
GraphAndNetwork
33
Transcriptomics
32
RNASeq
31
DifferentialExpression
30
BiomedicalInformatics
28
NetworkInference
27
GeneSetEnrichment
26
Proteomics
25
FunctionalGenomics
25
Sequencing
24
GeneRegulation
24
Clustering
24
ImmunoOncology
23
Visualization
20
Regression
19
Transcription
19
Microarray
19
Genetics
18
NetworkEnrichment
17
MultipleComparison
14
CellBiology
14
SingleCell
13
Normalization
13
Classification
12
DataImport
12
QualityControl
11
KEGG
11
Metabolomics
11
FunctionalPrediction
10
Epigenetics
10
Preprocessing
9
GenePrediction
9
Bayesian
9
r
8
AlternativeSplicing
8
TimeCourse
8
Annotation
8
FeatureExtraction
8
BatchEffect
7
GeneSignaling
7
ChIPSeq
7
GeneTarget
7
GO
7
GenomicVariation
7
DataRepresentation
7
PrincipalComponent
6
MathematicalBiology
6
DimensionReduction
6
DNAMethylation
6
SNP
5
GenomeAnnotation
5
Cheminformatics
5
Reactome
5
bioinformatics
5
OneChannel
5
DifferentialSplicing
5
StatisticalMethod
5
DNASeq
4
bioconductor
4
TwoChannel
4
ATACSeq
4
DifferentialMethylation
4
Coverage
4
CopyNumberVariation
4
mRNAMicroarray
4
MethylSeq
3
clustering
3
GeneticVariability
3
rstats
3
PooledScreens
3
Survival
3
WorkflowStep
3
Lipidomics
3
ProprietaryPlatforms
3
TranscriptomeVariant
3
DecisionTree
3
NeuralNetwork
3
CRISPR
3
Alignment
2
Microbiome
2
ExonArray
2
MicroRNAArray
2
genomics
2
biology
2
GenomeWideAssociation
2
PatternLogic
2
MotifDiscovery
2
ResearchField
2
r-package
2
network-science
2
genetics
2
ComparativeGenomics
2
mirna
2
Pharmacogenomics
2
GUI
2
networks
2