bioconductor.org "SystemsBiology" keyword
View the packages on the bioconductor.org package registry that are tagged with the "SystemsBiology" keyword.
CausalR 1.40.0
Causal network analysis methods5 versions - Latest release: 3 months ago - 17.8 thousand downloads total - 2 maintainers
SGCP 1.8.0
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...7 versions - Latest release: 3 months ago - 5.65 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
23 versions - Latest release: 19 days ago - 181 dependent packages - 3.6 million downloads total - 4 maintainers
edgeR 4.6.3
Empirical Analysis of Digital Gene Expression Data in R23 versions - Latest release: 19 days ago - 181 dependent packages - 3.6 million downloads total - 4 maintainers
progeny 1.30.0
Pathway RespOnsive GENes for activity inference from gene expression5 versions - Latest release: 3 months ago - 2 dependent packages - 40.7 thousand downloads total - 105 stars on GitHub - 1 maintainer
HPiP 1.14.0
Host-Pathogen Interaction Prediction5 versions - Latest release: 3 months ago - 6.42 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 2 dependent packages - 161 thousand downloads total - 301 stars on GitHub - 1 maintainer
microbiome 1.30.0
Microbiome Analytics5 versions - Latest release: 3 months ago - 2 dependent packages - 161 thousand downloads total - 301 stars on GitHub - 1 maintainer
wppi 1.16.0
Weighting protein-protein interactions5 versions - Latest release: 3 months ago - 8.06 thousand downloads total - 1 stars on GitHub - 1 maintainer
genomicInstability 1.14.0
Genomic Instability estimation for scRNA-Seq5 versions - Latest release: 3 months ago - 6.41 thousand downloads total - 4 stars on GitHub - 1 maintainer
CHRONOS 1.36.0
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis5 versions - Latest release: 3 months ago - 16.5 thousand downloads total - 1 maintainer
cytoMEM 1.12.0
Marker Enrichment Modeling (MEM)5 versions - Latest release: 3 months ago - 6.75 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 6.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 3 dependent packages - 61.5 thousand downloads total - 1 maintainer
hpar 1.50.0
Human Protein Atlas in R5 versions - Latest release: 3 months ago - 3 dependent packages - 61.5 thousand downloads total - 1 maintainer
Top 4.5% on bioconductor.org
5 versions - Latest release: 3 months ago - 2 dependent packages - 105 thousand downloads total - 1 maintainer
GENIE3 1.30.0
GEne Network Inference with Ensemble of trees5 versions - Latest release: 3 months ago - 2 dependent packages - 105 thousand downloads total - 1 maintainer
pfamAnalyzeR 1.8.0
Identification of domain isotypes in pfam data5 versions - Latest release: 3 months ago - 1 dependent package - 12.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
doseR 1.24.0
doseR5 versions - Latest release: 3 months ago - 9.78 thousand downloads total - 1 maintainer
dearseq 1.20.0
Differential Expression Analysis for RNA-seq data through a robust variance component test5 versions - Latest release: 3 months ago - 2 dependent packages - 16.6 thousand downloads total - 6 stars on GitHub - 1 maintainer
KnowSeq 1.22.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline5 versions - Latest release: 3 months ago - 10.7 thousand downloads total - 1 maintainer
artMS 1.26.0
Analytical R tools for Mass Spectrometry5 versions - Latest release: 3 months ago - 14.1 thousand downloads total - 1 maintainer
metaseqR2 1.20.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...5 versions - Latest release: 3 months ago - 9.84 thousand downloads total - 1 maintainer
magrene 1.10.0
Motif Analysis In Gene Regulatory Networks5 versions - Latest release: 3 months ago - 5.07 thousand downloads total - 1 stars on GitHub - 1 maintainer
SBGNview 1.22.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"5 versions - Latest release: 3 months ago - 14.1 thousand downloads total - 26 stars on GitHub - 1 maintainer
KBoost 1.16.0
Inference of gene regulatory networks from gene expression data5 versions - Latest release: 3 months ago - 6.21 thousand downloads total - 4 stars on GitHub - 1 maintainer
GenomicOZone 1.22.0
Delineate outstanding genomic zones of differential gene activity5 versions - Latest release: 3 months ago - 9.53 thousand downloads total - 1 maintainer
Top 3.1% on bioconductor.org
5 versions - Latest release: 3 months ago - 4 dependent packages - 115 thousand downloads total - 1 maintainer
RankProd 3.34.0
Rank Product method for identifying differentially expressed genes with application in meta-analysis5 versions - Latest release: 3 months ago - 4 dependent packages - 115 thousand downloads total - 1 maintainer
pathwayPCA 1.24.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection5 versions - Latest release: 3 months ago - 1 dependent package - 12.1 thousand downloads total - 11 stars on GitHub - 1 maintainer
easier 1.14.0
Estimate Systems Immune Response from RNA-seq data5 versions - Latest release: 3 months ago - 8.89 thousand downloads total - 1 maintainer
SPONGE 1.30.0
Sparse Partial Correlations On Gene Expression6 versions - Latest release: 3 months ago - 2 dependent packages - 12.7 thousand downloads total - 1 maintainer
vulcan 1.30.0
VirtUaL ChIP-Seq data Analysis using Networks5 versions - Latest release: 3 months ago - 13.1 thousand downloads total - 1 maintainer
sitadela 1.16.0
An R package for the easy provision of simple but complete tab-delimited genomic annotation from ...5 versions - Latest release: 3 months ago - 6.49 thousand downloads total - 0 stars on GitHub - 1 maintainer
sincell 1.40.0
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data5 versions - Latest release: 3 months ago - 20.6 thousand downloads total - 1 maintainer
Top 3.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 4 dependent packages - 193 thousand downloads total - 5 stars on GitHub - 1 maintainer
gage 2.58.0
Generally Applicable Gene-set Enrichment for Pathway Analysis5 versions - Latest release: 3 months ago - 4 dependent packages - 193 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
5 versions - Latest release: 3 months ago - 9 dependent packages - 600 thousand downloads total - 41 stars on GitHub - 1 maintainer
pathview 1.48.0
a tool set for pathway based data integration and visualization5 versions - Latest release: 3 months ago - 9 dependent packages - 600 thousand downloads total - 41 stars on GitHub - 1 maintainer
mdp 1.28.0
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their ...5 versions - Latest release: 3 months ago - 12.4 thousand downloads total - 1 maintainer
COCOA 2.22.0
Coordinate Covariation Analysis5 versions - Latest release: 3 months ago - 11.7 thousand downloads total - 1 maintainer
IsoformSwitchAnalyzeR 2.8.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...5 versions - Latest release: 3 months ago - 38.7 thousand downloads total - 1 maintainer
gCrisprTools 2.14.0
Suite of Functions for Pooled Crispr Screen QC and Analysis5 versions - Latest release: 3 months ago - 16.5 thousand downloads total - 1 maintainer
pmm 1.40.0
Parallel Mixed Model5 versions - Latest release: 3 months ago - 15.1 thousand downloads total - 1 maintainer
EGAD 1.36.0
Extending guilt by association by degree5 versions - Latest release: 3 months ago - 18.2 thousand downloads total - 1 maintainer
XINA 1.26.0
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis5 versions - Latest release: 3 months ago - 12.3 thousand downloads total - 1 maintainer
sRACIPE 2.0.1
Systems biology tool to simulate gene regulatory circuits6 versions - Latest release: 2 months ago - 9.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
MIRA 1.30.0
Methylation-Based Inference of Regulatory Activity5 versions - Latest release: 3 months ago - 1 dependent package - 15 thousand downloads total - 1 maintainer
SMITE 1.36.0
Significance-based Modules Integrating the Transcriptome and Epigenome5 versions - Latest release: 3 months ago - 16.2 thousand downloads total - 1 stars on GitHub - 2 maintainers
geva 1.16.0
Gene Expression Variation Analysis (GEVA)5 versions - Latest release: 3 months ago - 6.69 thousand downloads total - 2 stars on GitHub - 1 maintainer
netDx 1.20.0
Network-based patient classifier5 versions - Latest release: 3 months ago - 6.23 thousand downloads total - 1 maintainer
ceRNAnetsim 1.20.0
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)6 versions - Latest release: 2 months ago - 7.81 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 7.2% on bioconductor.org
7 versions - Latest release: 3 months ago - 1 dependent package - 39.5 thousand downloads total - 1 maintainer
Rcpi 1.44.0
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery7 versions - Latest release: 3 months ago - 1 dependent package - 39.5 thousand downloads total - 1 maintainer
epiNEM 1.32.0
epiNEM5 versions - Latest release: 3 months ago - 4 dependent packages - 16.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
rcellminer 2.30.1
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines6 versions - Latest release: about 19 hours ago - 21 thousand downloads total - 3 maintainers
Path2PPI 1.38.0
Prediction of pathway-related protein-protein interaction networks5 versions - Latest release: 3 months ago - 17.6 thousand downloads total - 1 maintainer
Pigengene 1.34.0
Infers biological signatures from gene expression data5 versions - Latest release: 3 months ago - 1 dependent package - 19.1 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
6 versions - Latest release: 3 months ago - 1 dependent package - 34.9 thousand downloads total - 1 maintainer
EGSEA 1.36.0
Ensemble of Gene Set Enrichment Analyses6 versions - Latest release: 3 months ago - 1 dependent package - 34.9 thousand downloads total - 1 maintainer
MWASTools 1.32.0
MWASTools: an integrated pipeline to perform metabolome-wide association studies5 versions - Latest release: 3 months ago - 1 dependent package - 19.3 thousand downloads total - 2 maintainers
Top 6.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 7 dependent packages - 74 thousand downloads total - 1 maintainer
viper 1.42.0
Virtual Inference of Protein-activity by Enriched Regulon analysis5 versions - Latest release: 3 months ago - 7 dependent packages - 74 thousand downloads total - 1 maintainer
iNETgrate 1.6.0
Integrates DNA methylation data with gene expression in a single gene network4 versions - Latest release: 3 months ago - 4.52 thousand downloads total - 65 stars on GitHub - 1 maintainer
cogena 1.42.0
co-expressed gene-set enrichment analysis5 versions - Latest release: 3 months ago - 23 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
6 versions - Latest release: 3 months ago - 4 dependent packages - 57.2 thousand downloads total - 1 maintainer
RedeR 3.4.0
Interactive visualization and manipulation of nested networks6 versions - Latest release: 3 months ago - 4 dependent packages - 57.2 thousand downloads total - 1 maintainer
DeMAND 1.38.0
DeMAND5 versions - Latest release: 3 months ago - 15.8 thousand downloads total - 2 maintainers
GmicR 1.22.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...5 versions - Latest release: 3 months ago - 9.81 thousand downloads total - 1 maintainer
rain 1.42.0
Rhythmicity Analysis Incorporating Non-parametric Methods5 versions - Latest release: 3 months ago - 24.6 thousand downloads total - 1 maintainer
roastgsa 1.6.0
Rotation based gene set analysis4 versions - Latest release: 3 months ago - 4.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
transcriptogramer 1.30.0
Transcriptional analysis based on transcriptograms5 versions - Latest release: 3 months ago - 13.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
paxtoolsr 1.42.0
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons5 versions - Latest release: 2 months ago - 27.5 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
14 versions - Latest release: 2 months ago - 322 dependent packages - 5.97 million downloads total - 1 maintainer
limma 3.64.1
Linear Models for Microarray and Omics Data14 versions - Latest release: 2 months ago - 322 dependent packages - 5.97 million downloads total - 1 maintainer
DeProViR 1.4.0
A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Prot...4 versions - Latest release: 2 months ago - 1.78 thousand downloads total - 1 stars on GitHub - 1 maintainer
BioCor 1.32.0
Functional similarities5 versions - Latest release: 2 months ago - 18.6 thousand downloads total - 14 stars on GitHub - 1 maintainer
MOGAMUN 1.18.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks5 versions - Latest release: 2 months ago - 7.53 thousand downloads total - 12 stars on GitHub - 1 maintainer
dominoSignal 1.2.0
Cell Communication Analysis for Single Cell RNA Sequencing2 versions - Latest release: 2 months ago - 2.01 thousand downloads total - 5 stars on GitHub - 1 maintainer
COTAN 2.8.5
COexpression Tables ANalysis18 versions - Latest release: 6 days ago - 8.52 thousand downloads total - 17 stars on GitHub - 1 maintainer
mnem 1.24.0
Mixture Nested Effects Models5 versions - Latest release: 3 months ago - 4 dependent packages - 13.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
epidecodeR 1.16.0
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation5 versions - Latest release: 3 months ago - 6.74 thousand downloads total - 3 stars on GitHub - 1 maintainer
seqArchR 1.12.0
Identify Different Architectures of Sequence Elements5 versions - Latest release: 3 months ago - 1 dependent package - 6.34 thousand downloads total - 1 stars on GitHub - 1 maintainer
RIVER 1.32.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)5 versions - Latest release: 3 months ago - 13.5 thousand downloads total - 10 stars on GitHub - 1 maintainer
scQTLtools 1.0.3
An R package for single-cell eQTL analysis and visualization3 versions - Latest release: about 1 month ago - 1.44 thousand downloads total - 0 stars on GitHub - 1 maintainer
BioNERO 1.16.0
Biological Network Reconstruction Omnibus7 versions - Latest release: 3 months ago - 1 dependent package - 19.8 thousand downloads total - 29 stars on GitHub - 1 maintainer
rsemmed 1.18.0
An interface to the Semantic MEDLINE database5 versions - Latest release: 2 months ago - 7.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
diggit 1.40.0
Inference of Genetic Variants Driving Cellular Phenotypes5 versions - Latest release: 2 months ago - 17.9 thousand downloads total - 1 maintainer
DEsubs 1.34.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...5 versions - Latest release: 3 months ago - 15.8 thousand downloads total - 2 maintainers
regutools 1.20.0
regutools: an R package for data extraction from RegulonDB5 versions - Latest release: 3 months ago - 8.67 thousand downloads total - 5 stars on GitHub - 1 maintainer
PrInCE 1.24.0
Predicting Interactomes from Co-Elution5 versions - Latest release: 3 months ago - 10.1 thousand downloads total - 6 stars on GitHub - 1 maintainer
GenomicSuperSignature 1.16.1
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases6 versions - Latest release: 3 months ago - 7.45 thousand downloads total - 12 stars on GitHub - 1 maintainer
protGear 1.12.0
Protein Micro Array Data Management and Interactive Visualization5 versions - Latest release: 3 months ago - 7.62 thousand downloads total - 1 stars on GitHub - 1 maintainer
syntenet 1.10.0
Inference And Analysis Of Synteny Networks8 versions - Latest release: 3 months ago - 1 dependent package - 7.84 thousand downloads total - 30 stars on GitHub - 1 maintainer
INSPEcT 1.38.0
Modeling RNA synthesis, processing and degradation with RNA-seq data6 versions - Latest release: 3 months ago - 21.3 thousand downloads total - 2 maintainers
CCPlotR 1.6.0
Plots For Visualising Cell-Cell Interactions4 versions - Latest release: 3 months ago - 4.5 thousand downloads total - 44 stars on GitHub - 1 maintainer
geneplast 1.34.0
Evolutionary and plasticity analysis of orthologous groups5 versions - Latest release: 3 months ago - 1 dependent package - 16.1 thousand downloads total - 1 maintainer
OmnipathR 3.16.0
OmniPath web service client and more7 versions - Latest release: 3 months ago - 3 dependent packages - 44 thousand downloads total - 1 maintainer
MouseFM 1.18.0
In-silico methods for genetic finemapping in inbred mice6 versions - Latest release: 3 months ago - 9.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
rScudo 1.24.0
Signature-based Clustering for Diagnostic Purposes6 versions - Latest release: 3 months ago - 9.68 thousand downloads total - 4 stars on GitHub - 1 maintainer
MOMA 1.20.0
Multi Omic Master Regulator Analysis5 versions - Latest release: 3 months ago - 8.62 thousand downloads total - 5 stars on GitHub - 1 maintainer
IMMAN 1.28.0
Interlog protein network reconstruction by Mapping and Mining ANalysis5 versions - Latest release: 3 months ago - 11.4 thousand downloads total - 1 maintainer
MEIGOR 1.42.0
MEIGOR - MEtaheuristics for bIoinformatics Global Optimization7 versions - Latest release: 3 months ago - 2 dependent packages - 21.5 thousand downloads total - 1 maintainer
MIRit 1.4.1
Integrate microRNA and gene expression to decipher pathway complexity5 versions - Latest release: about 2 months ago - 3.69 thousand downloads total - 1 stars on GitHub - 1 maintainer
mistyR 1.16.0
Multiview Intercellular SpaTial modeling framework6 versions - Latest release: 3 months ago - 8.81 thousand downloads total - 44 stars on GitHub - 1 maintainer
bnem 1.16.0
Training of logical models from indirect measurements of perturbation experiments5 versions - Latest release: 3 months ago - 7.04 thousand downloads total - 2 stars on GitHub - 1 maintainer
oppar 1.36.1
Outlier profile and pathway analysis in R6 versions - Latest release: 2 months ago - 14.3 thousand downloads total - 1 maintainer
PhenoGeneRanker 1.16.0
PhenoGeneRanker: A gene and phenotype prioritization tool5 versions - Latest release: 3 months ago - 5.74 thousand downloads total - 1 maintainer
LOLA 1.38.0
Locus overlap analysis for enrichment of genomic ranges5 versions - Latest release: 3 months ago - 5 dependent packages - 31.3 thousand downloads total - 1 maintainer
ReactomeGSA 1.22.0
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis6 versions - Latest release: 3 months ago - 19.4 thousand downloads total - 25 stars on GitHub - 1 maintainer
nempi 1.16.0
Inferring unobserved perturbations from gene expression data5 versions - Latest release: 3 months ago - 6.41 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: 8 months ago - 1 dependent package - 10.7 thousand downloads total - 21 stars on GitHub - 1 maintainer
IntOMICS 1.4.0 removed
Integrative analysis of multi-omics data to infer regulatory networks3 versions - Latest release: about 1 year ago - 1.07 thousand downloads total - 0 stars on GitHub - 1 maintainer
Related Keywords
Software
110
GeneExpression
56
Network
45
GraphAndNetwork
32
Pathways
31
RNASeq
30
Transcriptomics
30
DifferentialExpression
29
BiomedicalInformatics
28
NetworkInference
27
FunctionalGenomics
25
GeneSetEnrichment
25
Proteomics
25
GeneRegulation
24
ImmunoOncology
23
Sequencing
23
Clustering
22
Transcription
19
Microarray
18
Regression
18
Genetics
18
NetworkEnrichment
17
Visualization
16
CellBiology
14
MultipleComparison
14
Normalization
12
SingleCell
12
DataImport
12
Classification
12
KEGG
11
FunctionalPrediction
10
QualityControl
10
Epigenetics
10
GenePrediction
9
Bayesian
9
Metabolomics
9
TimeCourse
8
r
8
FeatureExtraction
8
Preprocessing
8
AlternativeSplicing
8
GenomicVariation
7
ChIPSeq
7
BatchEffect
7
Annotation
7
GeneSignaling
7
GeneTarget
7
PrincipalComponent
6
DNAMethylation
6
GO
6
MathematicalBiology
6
Cheminformatics
5
GenomeAnnotation
5
OneChannel
5
DataRepresentation
5
SNP
5
DimensionReduction
5
DifferentialSplicing
5
Reactome
5
DNASeq
4
CopyNumberVariation
4
StatisticalMethod
4
DifferentialMethylation
4
mRNAMicroarray
4
bioinformatics
4
ATACSeq
4
Coverage
4
TwoChannel
4
TranscriptomeVariant
3
DecisionTree
3
NeuralNetwork
3
Survival
3
GeneticVariability
3
MethylSeq
3
CRISPR
3
Lipidomics
3
ProprietaryPlatforms
3
clustering
3
WorkflowStep
3
PooledScreens
3
rstats
3
bioconductor
3
ResearchField
2
ExonArray
2
SomaticMutation
2
networks
2
GenomeWideAssociation
2
MicroRNAArray
2
genomics
2
ComparativeGenomics
2
PatternLogic
2
biology
2
Pharmacogenetics
2
Pharmacogenomics
2
GUI
2
gene
2
genetics
2
mirna
2
r-package
2
ExperimentHubSoftware
2