Biocview "SystemsBiology"

A metagenomic pipeline for systems biology
A metagenomic pipeline for systems biology
Analysis of 4sU-seq and RNA-seq time-course data
Analysis of 4sU-seq and RNA-seq time-course data
Analysis of 4sU-seq and RNA-seq time-course data
An R interface for computational modeling of tumor progression
An R interface for computational modeling of tumor progression
An R interface for computational modeling of tumor progression
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annotate and Visualize Isoform Switches with Functional Consequences (from RNA-seq data)
A Systems Biology Approach for Drug Repurposing
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
Causal network analysis methods
Causal network analysis methods
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
DeMAND
DeMAND
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
epiNEM
epiNEM
epiNEM
Evolutionary and plasticity analysis based on orthologous groups distribution
Evolutionary and plasticity analysis based on orthologous groups distribution
Extending guilt by association by degree
Extending guilt by association by degree
Extending guilt by association by degree
Finding Mutually Exclusive Groups of Alterations in Cancer Datasets
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Functional similarities
Functional similarities
Functional similarities
Functions for Cytoscape Automation
GEne Network Inference with Ensemble of trees
GEne Network Inference with Ensemble of trees
Generally Applicable Gene-set Enrichment for Pathway Analysis
Generally Applicable Gene-set Enrichment for Pathway Analysis
Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
Identification of Functional Epigenetic Modules
Identification of Functional Epigenetic Modules
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference of Genetic Variants Driving Cellular Phenotypes
Inference of Genetic Variants Driving Cellular Phenotypes
Infers biological signatures from gene expression data
Infers biological signatures from gene expression data
Integrative analysis pipeline for pooled CRISPR functional genetic screens
Interlog protein network reconstruction by Mapping and Mining ANalysis
Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics
Location overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Matched Interaction across Tissues (MIxT) data analysis
MEIGO - MEtaheuristics for bIoinformatics Global Optimization
MEIGO - MEtaheuristics for bIoinformatics Global Optimization
Methylation-Based Inference of Regulatory Activity
Methylation-Based Inference of Regulatory Activity
Microbiome Analytics
Microbiome Analytics
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
MWASTools: an integrated pipeline to perform metabolome-wide association studies
MWASTools: an integrated pipeline to perform metabolome-wide association studies
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
Parallel Mixed Model
Parallel Mixed Model
Pathway-based data integration of omics data
Pathway-based data integration of omics data
Pathway-based data integration of omics data
Pathway-based data integration of omics data
Pathway RespOnsive GENes for activity inference from gene expression
Pathway RespOnsive GENes for activity inference from gene expression
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Plot the effect of one omics data on other omics data along the chromosome
Plot the effect of one omics data on other omics data along the chromosome
Prediction of pathway-related protein-protein interaction networks
Prediction of pathway-related protein-protein interaction networks
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Rank Product method for identifying differentially expressed genes with application in meta-analysis
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
Rhythmicity Analysis Incorporating Non-parametric Methods
Rhythmicity Analysis Incorporating Non-parametric Methods
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Sparse Partial Correlations On Gene Expression
Sparse Partial Correlations On Gene Expression
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Tools for microbiome analysis
training of logical models from indirect measurements of perturbation experiments
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
VirtUaL ChIP-Seq data Analysis using Networks
VirtUaL ChIP-Seq data Analysis using Networks
Virtual Inference of Protein-activity by Enriched Regulon analysis
Virtual Inference of Protein-activity by Enriched Regulon analysis
Virtual Inference of Protein-activity by Enriched Regulon analysis