Search Results for "gene regulatory networks" - Page 2
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Showing 81 open source projects for "gene regulatory networks"
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GenNet
A Tool for Qualitative and Quantitative Modeling of Gene Regulatory Ne
A Tool for Qualitative and Quantitative Modeling of Gene Regulatory Networks. GenNet is a Java based tool called that facilitate the model checking user by providing a unique GUI layout for both qualitative and quantitative modeling of GRNs. GenNet also assists the modeling users by providing some extra features i.e. CTL editor, parameters filtering and input/output files management. Download pre-installed GenNet Virtual Box Image here https://www.dropbox.com/s/9ryvs1f22zc181y/GenNet-1.3.28... -
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CoGA
R package for differential co-expression analysis
CoGA (Co-expression Graph Analyzer) is an R package to identify differentially co-expressed gene sets between two phenotypes. The software infers gene regulatory networks from gene expression data, and compares structural properties of the inferred networks based on their spectrum distributions. It also compares the networks in terms of their gene centralities, clustering coefficients and shortest path lengths. In addition to the differential co-expression analyses, the tool provides graphical... -
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nagnag
Identifyng and Quantifying NAGNAG Alternative Splicing
The NAGNAG alternative splicing is a regulatory process that controls the mRNA splicing from one gene. NAGNAG alternative splicing has attracted intensive attentions for last decades because of its unique property: inclusion or exclusion of three nucleotides results in difference of one or two amino acids in the final proteins. -
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sRNA gene regulatory network generator
Plant small RNA mediated gene regulatory network generator
A workflow of construction of small RNA mediated gene regulatory network using computational methods. The regulatory network shows differential expressed small RNAs and their potential targets as well as the gene expression information of potential targets. The workflow is written in Perl and run on Linux System. -
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DESN
Differential activE sub-Network (DEN): R/Bioconductor based package
Living cells are complex, dynamic, self-regulatory, interactive systems, showing differential states across time and space. Complexity of cellular systems is highlighted with the multi-layered regulatory mechanisms involving the interactions between bio-molecules (such as DNA, RNA, mi-RNA and proteins). These interactions are analyzed in the form of static networks. Likewise, number of experimental techniques like microarray, RNASeq allows quantification of cellular dynamics and aid... -
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diggit
R package for DIGGIT algorithm
DIGGIT identify genetic variants associated with drivers of specific physiopathologic states. I computes the statistical association between the presence of genetic variants (CNV or SNP) and the activity of proteins driving physiologic or pathologic phenotype. It requires large gene expression and genetic variants datasets and depends on context-specific regulatory networks including transcriptional interactomes (usually reverse engineered by the ARACNe algorithm) and post-translational... -
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Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.
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rnea
Regulatory Network Enrichment Analysis
Given a differential expression file RNEA extracts lists of prioritized TFs, miRNAs, KEGG pathways and categories and GO terms and at the same time it combines them at an HTML file. Most importantly a regulatory subnetwork is extracted showing how the activated regulators interact with their target genes and between each other. In this way, given a genome-wide expression experiment, RNEA prioritizes important regulatory and functional components. It also succeeds to reconstruct meaningful... -
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ESTReMo
An evolutionary simulator of transcription regulatory networks
ESTReMo is a genetic algorithm-based simulator to explore the evolution of transcription factors and their binding motifs on realistic genomic backgrounds. -
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miRStat
identification of common sets of microRNAs for groups of genes
miRStat enables identification of regulatory microRNA targeting several genes in a custom gene group. This Python application is based on the TargetScan 6.2 microRNA target prediction data. Conserved and Nonconserved site context+ scores files are required (unzip and place to directory with program). Available at http://targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61 -
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bLARS
bLARS is a GRN inference algorithm.
bLARS infers gene regulatory network (GRN) from gene-expression data. It uses a modification in Least Angle Regression (LARS) algorithm to allow more flexibility in tx-factor-gene regulations. -
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RIPE (Regulatory network Inference from joint Perturbation and Expression data) is a novel three-step method that integrates both perturbation data and steady state gene expression data in order to estimate a regulatory network. The ripe package is written in R, with additional functionality provided by a MATLAB executable file. The executable file uses a runtime engine called the MATLAB Compiler Runtime (MCR). The executable for different architectures is distributed on this site together...
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nail_systems_biology
NAIL is a toolset for network analysis in the life sciences
The NAIL (Network Analysis and Inference Library) project is a set of tools for solving problems in the life sciences using network (graph) approaches. NAIL includes methods for creating networks, analysing and comparing networks, and for visualising or presenting the results. These methods are designed as self-contained platform-independent components which can be called either from another program, or from a command line. Modelling biological systems as networks (graphs) is becoming... -
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GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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PANDA
Passing Attributes between Networks for Data Assimilation
PANDA (Passing Attributes between Networks for Data Assimilation), is a message-passing model to gene regulatory network reconstruction. PANDA integrates multiple sources of biological data, including protein-protein interaction, gene expression, and sequence motif information, in order to reconstruct genome-wide, condition-specific regulatory networks. PANDA is also available in other programming languages, including: MATLAB/Octave: (1) https://drive.google.com/a/channing.harvard.edu... -
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PRUNET is a user-friendly software tool designed to address the contextualization of a prior knowledge gene regulatory networks (PKN) to specific experimental conditions. As the input, the algorithm takes a PKN and the expression profile of two given stable states or cellular phenotypes.
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budden2014predictive
Scripts and supplementary data for budden2014predictive manuscript
Scripts and supplementary data for the manuscript "Predictive modeling of gene expression from transcriptional regulatory elements" -
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A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on )nding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast method, HopeMap, for network alignment...
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grn_inference_multigpu
This project is a exhaustive search algoritm for multiple GPUs
Gene regulatory networks (GRN) inference is an important bioinformatics problem in which the gene interactions need to be deduced from gene expression data, such as microarray data. <br> Feature selection methods can be applied to this problem. A feature selection technique is composed by two parts: a search algorithm and a criterion function. Among the search algorithms already proposed, there is the exhaustive search where the best feature subset is returned, although its computational... -
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VariabilityAnalysisInNetworks
An R package for identifying biologically perturbed networks
The VAN package enables an integrative analysis of (i) gene expression data with protein-protein interaction networks or (ii) gene and microRNA expression data with microRNA-gene interaction networks to identify biologically perturbed networks. -
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rTRM
Identification of transcriptional regulatory modules (TRMs)
This R package can be used to identify TRMs using experimental evidence from a single ChIP-seq experiment. It combines computational predicted transcription factor (TF) binding sites, gene expression and protein-protein interaction (PPI) data and use it to predict TRMs. -
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Kinsolver
A simulator for biochemical and gene regulatory networks
Research Article: http://www.sciencedirect.com/science/article/pii/S0898122108006287 -
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Genet_Package
Identifying Gene Signatures with Implication Networks
Identifying Gene Signatures with Implication Networks -
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AMBIENT
Find active modules in metabolic networks using high-throughput data
IMPORTANT: Since publication of the AMBIENT method in BMC Sys Bio, several updates have been made. If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest! AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have... -
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GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods. GNW was used to generate the community-wide DREAM3, DREAM4 and DREAM5 In Silico Challenges.