Biocview "SystemsBiology"

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
A metagenomic pipeline for systems biology
Analysis and Visualisation of the Human Phenotype Ontology
Analysis of alternative poly A site usage
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analyze Microbiome Data
An interface to the Semantic MEDLINE database
An interface to the Semantic MEDLINE database
An R interface for computational modeling of tumor progression
An R interface for computational modeling of tumor progression
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms
A set of methods and tools for comprehensive analysis of phosphoproteomics data
A set of methods and tools for comprehensive analysis of phosphoproteomics data
A Systems Biology Approach for Drug Repurposing
A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
Automated genomic fine-mapping
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Biological Network Analysis
Biological Network Analysis
Biological Network Reconstruction Omnibus
Causal network analysis methods
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
Client for the Reactome Analysis Service for comparative multi-omics gene set 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
COexpression Tables ANalysis
COexpression Tables ANalysis
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
Compare Patient Samples to Cell Line Models Using Molecular Data and Weighted Similarity
Contains utils for loading and manipulating two-layers structure network models
Contains utils for loading and manipulating two-layers structure network models
Contains utils for loading and manipulating two-layers structure network models
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Coordinate Covariation Analysis
CoRegFlux
CoRegFlux
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
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
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
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients
Detect marker panel from scRNA-seq profile
Detect marker panel from scRNA-seq profile
Differential Expression Analysis for RNA-seq data through a robust variance component test
Discriminant Analysis for Evolutionary Inference
Discriminant Analysis for Evolutionary Inference
doseR
doseR
doseR
doseR
doseR
(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
echoverse module: Annotate fine-mapping results
echoverse module: Create package dependency graphs
echoverse module: echoversePackageTitle
echoverse module: Fine-mapping data access and formatting
echoverse module: Fine-mapping functions
echoverse module: Locus plot creation for fine-mapping and colocalization studies
echoverse module: Locus plot creation for fine-mapping and colocalization studies
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
epiNEM
epiNEM
Estimate Systems Immune Response from RNA-seq data
Evolutionary and plasticity analysis of orthologous groups
EWCE for Multiple Gene Lists
EWCE for Multiple Gene Lists
Extending guilt by association by degree
Extending guilt by association by degree
Finding Mutually Exclusive Groups of Alterations in Cancer Datasets
Find microbial interactions
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
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Functional similarities
Functional similarities
Functions for Cytoscape Automation
Gene Expression Variation Analysis (GEVA)
Gene Expression Variation Analysis (GEVA)
GEne Network Inference with Ensemble of trees
GEne Network Inference with Ensemble of trees
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
GeneVyuha is a systems biology tool to study the role of noise and parameter variation in gene regulatory circuits.
Genomic Instability estimation for scRNA-Seq
Host-Pathogen Interaction Prediction
Human Protein Atlas in R
Identification of Functional Epigenetic Modules
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Identify Different Architectures of Sequence Elements
Identify Different Architectures of Sequence Elements
Inference And Analysis Of Synteny Networks
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference of gene regulatory networks from gene expression data
Inference of Genetic Variants Driving Cellular Phenotypes
Inferring unobserved perturbations from gene expression data
Infers biological signatures from gene expression data
In-silico methods for genetic finemapping in inbred mice
In-silico methods for genetic finemapping in inbred mice
In-silico methods for genetic finemapping in inbred mice
Integrative analysis of multi-omics data to infer regulatory networks
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Interlog protein network reconstruction by Mapping and Mining ANalysis
Interlog protein network reconstruction by Mapping and Mining ANalysis
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
Landscape Single Cell Entropy
Linear Models for Microarray Data
Linear Models for Microarray Data
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Marker Enrichment Modeling (MEM)
Marker Enrichment Modeling (MEM)
Matched Interaction across Tissues (MIxT) data analysis
Mean Alterations Using Discrete Expression
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
Mining, Calling, and Importing Epigenomic Peaks in R
Mixture Nested Effects Models
Mixture Nested Effects Models
Modeling RNA synthesis, processing and degradation with RNA-seq data
Modeling RNA synthesis, processing and degradation with RNA-seq data
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
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
Motif Analysis In Gene Regulatory Networks
Multi Omic Master Regulator Analysis
Multi Omic Master Regulator Analysis
Multi-Omics (time-course) network-based integration and interpretation
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
Multiview Intercellular SpaTial modeling framework
Multiview Intercellular SpaTial modeling framework
MWASTools: an integrated pipeline to perform metabolome-wide association studies
netboxr
netboxr
Network-based patient classifier
Network-based patient classifier
Network Perturbation Amplitude
Network Perturbation Amplitude
OmniPath web service client
OmniPath web service client and more
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
Overlay omics data onto SBGN pathway diagram
packageTitle
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 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
Perform co-DE gene analysis
PhenoGeneRanker: A gene and phenotype prioritization tool
Plot the effect of one omics data on other omics data along the chromosome
Predicting Interactomes from Co-Elution
Predicting Interactomes from Co-Elution
Predicting Interactomes from Co-Elution
Prediction of pathway-related protein-protein interaction networks
Preprocess epigenomic data for downstream analysis
Preprocess epigenomic data for downstream analysis
Probabilistic combinatorial nested effects model
Protein Micro Array Data Management and Interactive Visualization
Random walk with restart on multiplex and heterogeneous Networks
Random walk with restart on multiplex and heterogeneous Networks
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Rapid Reconstruction of Time-Varying Gene Regulatory Networks
Rapid Reconstruction of Time-Varying Gene Regulatory Networks
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
regutools: an R package for data extraction from RegulonDB
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 the statistical assessment of cell state hierarchies from single-cell RNA-seq data
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
Signature-based Clustering for Diagnostic Purposes
Signature-based Clustering for Diagnostic Purposes
Signature-based Clustering for Diagnostic Purposes
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Single Cell Entropy
Software set for alignment of biological replicate data
Software set for alignment of biological replicate data
Sparse Partial Correlations On Gene Expression
Sparse Partial Correlations On Gene Expression
Sparse Partial Correlations On Gene Expression
SPIA-PCC: Signaling pathway impact analysis incorporated the change of Pearson correla-tion coefficient between two groups
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
Systems biology tool to simulate gene regulatory circuits
Systems biology tool to simulate gene regulatory circuits
Systems biology tool to simulate gene regulatory circuits
Systems biology tool to simulate gene regulatory circuits
Systems biology tool to simulate gene regulatory circuits
Tools for microbiome analysis
Tools for the Analysis of Ratiometric Data
Training of logical models from indirect measurements of perturbation experiments
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
Weighting protein-protein interactions