Biocview "SystemsBiology"

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

Analyze Microbiome Data

An interface to the Semantic MEDLINE database

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 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 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

Automated genomic fine-mapping

Automatic calculation of literature relevance of genes

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

coexnet: An R package to build CO-EXpression NETworks from Microarray Data

co-expressed gene-set enrichment analysis

COexpression Tables ANalysis

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

Coordinate Covariation Analysis

CoRegFlux

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

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

Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

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

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

Empirical Analysis of Digital Gene Expression Data in R

Ensemble of Gene Set Enrichment Analyses

epiNEM

Estimate Systems Immune Response from RNA-seq data

Evolutionary and plasticity analysis of orthologous groups

EWCE for Multiple Gene Lists

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

Functional similarities

Functions for Cytoscape Automation

Gene Expression Variation Analysis (GEVA)

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

Genetic inteRaction and EssenTiality neTwork mApper

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 Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

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

Integrative analysis of multi-omics data to infer regulatory networks

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Interlog protein network reconstruction by Mapping and Mining ANalysis

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

Landscape Single Cell Entropy

Linear Models for Microarray Data

Locus overlap analysis for enrichment of genomic ranges

Marker Enrichment Modeling (MEM)

Matched Interaction across Tissues (MIxT) data analysis

Mean Alterations Using Discrete Expression

MEIGO - MEtaheuristics for bIoinformatics Global Optimization

MEIGOR - MEtaheuristics for bIoinformatics Global Optimization

Methylation-Based Inference of Regulatory Activity

Microbiome Analytics

Mining, Calling, and Importing Epigenomic Peaks in R

Mixture Nested Effects Models

Modeling RNA synthesis, processing and degradation with RNA-seq data

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 Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Motif Analysis In Gene Regulatory Networks

Multi Omic Master Regulator Analysis

Multi-Omics (time-course) network-based integration and interpretation

Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

Multi-Scale Target Explorer

Multiview Intercellular SpaTial modeling framework

MWASTools: an integrated pipeline to perform metabolome-wide association studies

netboxr

Network-based patient classifier

Network Perturbation Amplitude

OmniPath web service client

OmniPath web service client and more

Outlier profile and pathway analysis in R

Overlay omics data onto SBGN pathway diagram

Parallel Mixed Model

Pathway-based data integration of omics data

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

Prediction of pathway-related protein-protein interaction networks

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

Rank Product method for identifying differentially expressed genes with application in meta-analysis

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines

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 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"

Signature-based Clustering for Diagnostic Purposes

Significance-based Modules Integrating the Transcriptome and Epigenome

Single Cell Entropy

Software set for alignment of biological replicate data

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

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

Transcriptional analysis based on transcriptograms

VirtUaL ChIP-Seq data Analysis using Networks

Virtual Inference of Protein-activity by Enriched Regulon analysis

Weighting protein-protein interactions

Biocview "SystemsBiology"

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