Search Results for "gene set enrichment analysis"
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Showing 37 open source projects for "gene set enrichment analysis"
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enrichmentpipeline
enrichment analysis for customized organisms
Do Gene set enrichment analysis for any organisms. -
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
* GSA-SNP2 is a successor of GSA-SNP (Nam et al. 2010, NAR web server issue). GSA-SNP2 accepts human GWAS summary data (rs numbers, p-values) or gene-wise p-values and outputs pathway genesets ‘enriched’ with genes associated with the given phenotype. It also provides both local and global protein interaction networks in the associated pathways. * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data using... -
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Clustergrammer
An interactive heatmap visualization built using D3.js
... interactive visualizations that enable intuitive exploration of high-dimensional data and has several biology-specific features (e.g. enrichment analysis, see Biology-Specific Features) to facilitate the exploration of gene-level biological data. -
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Panacea
PAN And Core-gEnome Analysis
A tool to calculate the Pan-Genome of a set of annotated genomes -
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IGSA
Individual Gene Sets Analysis
IGSA (Individual Gene Sets Analysis) is an application software based on Java and R that leverages a powerful analytical capacity. It can be used for gene sets enrichment and samples clustering. In gene sets enrichment, IGSA takes account of the heterogeneity of genes expression in samples and the homogeneity at the functional level, trying to pick out more particular and more significant gene sets. In sample clustering, IGSA clusters the samples based on the significant pathways rather than... -
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HPOSim
Analysis phenotypic similarity between genes and between diseases
This package implements multiple similarity measures for HPO terms, genes and diseases. It is aiming at phenotype analysis for gene sets and disease sets. Functions for HPO enrichment analysis is also provided. -
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AccNET
AccNET: Accessory Genome Constellation Network.
AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms. Using the proteomes of these organisms, AccNET create a bipartite network compatible with common network analysis platforms. AccNET collects phylogenetic and functional information in a network improving the analysis capability. Networks offer a new perspective of organism organization through elements acquired by horizontal gene transfers and not constricted by hierarchical... -
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Zika-RNAseq-Pipeline
An open RNA-Seq data analysis pipeline tutorial
... configuration overhead. The pipeline enables the extraction of knowledge from typical RNA-seq studies by generating interactive principal component analysis (PCA) and hierarchical clustering (HC) plots, performing enrichment analyses against over 90 gene set libraries, and obtaining lists of small molecules that are predicted to either mimic or reverse the observed changes in mRNA expression. -
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PALM
Probabilistic natural mapping for gene based association study.
PALM is a software that conducts gene-based association analysis. PALM exploits Hidden Markov Models (HMM) to capture the inner genomic structures. Then, unique gene features (termed "palm prints") are extracted for each gene set by calculating the natural gradient. Then palm-prints are tested with chi-square significance test. -
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CorNetMap
A tool for Gene Expression Correlation Network
Capabilities of CorNetMap: 1. Read data as tab-delimited text file. Can be used for analysis of any data set beyond gene expression. 2. Capable of both two-dimensional and multidimensional data analysis. 3. Calculate Pearson correlation and cross-correlation for analysis data with phase difference. 4. Generate correlation Heat-map and draws network map. 5. Save correlation data as text file. How to use and doccumentation: https://sourceforge.net/projects/cornetmap/files... -
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... modularity and robustness is conserved in a large set of randomly structured networks. The app provides various visualization modes to better elucidate topological relations between modules, and tabular results of centrality and gene ontology enrichment analyses of modules.
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goSTAG
Gene Ontology Subtrees to Tag and Annotate Genes within a set
We developed goSTAG for utilizing Gene Ontology Subtrees to Tag and Annotate Genes that are part of a set. Given gene lists, goSTAG performs GO enrichment analysis and clusters the GO terms based on the p-values from the significance tests. GO subtrees are constructed for each cluster, and the term that has the most paths to the root within the subtree is used to tag and annotate the cluster. -
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BAGEL: analysis of gene knockout screens
BAGEL: Bayesian Analysis of Gene EssentiaLity
BAGEL: software for Bayesian analysis of gene knockout screens using pooled library CRISPR or RNAi. BAGEL is a Bayesian classifier for pooled library genetic perturbation screens, using either CRISPR-Cas9 or shRNA libraries. It uses training sets of known essential and nonessential genes to estimate what the fold change distribution of an essential or nonessential gene should look like. Then, for each uncharacterized gene, it takes all observations of reagents targeting that gene (guide RNA... -
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PGAP
PGAP is a pipeline for pan-genome analysis.
PGAP is a pan-genomes analysis pipeline developed with Perl. It could perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters. -
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GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data.
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GSEAlite
Gene Set Enrichment Analysis, plot and analysis (p, FDR, ES, NES)
This is my implementation of the Gene Set Enrichment Analysis methodology (http://www.broadinstitute.org/gsea/index.jsp; Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550) and Mootha, Lindgren, et al. (2003, Nat Genet 34, 267-273)). The package gives access to the typical plot function: Enrichment Analysis and to the analysis of list of gene sets. p-values, FDR, ES and NES are computed. A read.gmt function allows to load gene set collection from MSigDB (http://www.broadinstitute.org... -
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A Tool for Retrieval, Visualization and Analysis of biological Pathways. Import a Gene or Protein Set from any Excel file. Automatically find signaling Pathways from KEGG. Integrate your Data in Seconds with a live interactive Force-directed Layout.
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Modular Single-set Enrichment Test
A randomization testing script for genetic enrichment analysis
The Modular Single-set Enrichment Test (MSET) is a randomization testing script written in R that allows the user to statistically assess overrepresentation of any gene list of interest within a list of significant gene results from an expression study. MSET uses a tcltk graphical user interface and is optimized for use in Windows operating systems. It also works in OS X, but requires the installation of the XQuartz architecture (https://xquartz.macosforge.org/trac/wiki) to enable tcltk... -
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GO analysis with continuous measures
THIS REPOSITORY HAS BEEN MOVED TO GITHUB
Download the latest updates from https://github.com/z0on/GO_MWU This project is about gene expression analysis. In contrast to most other "GO enrichment analysis" methods, this one does not look for GO categories enriched within a list of "significant" genes. Instead, it uses a rank-based test to measure how much each GO category is enriched with either up or down-regulated genes. The significant GO categories are clustered based on the number of genes shared between them and the results... -
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ZGST
Ziemann's Gene Set Test
ZGST is a gene set analysis software run in the Unix Shell that is analogous to GSEA. It us designed to be faster, more amenable to pipeline automation and use less RAM. -
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Pointer GSA
Pointer - Gene Set Analysis for Genome Wide Association Study data
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rnea
Regulatory Network Enrichment Analysis
... subnetworks of gene regulation, offering further ways of analyzing the data based on network theory. -
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Multi-Pipeline Gene Expression Analysis
Helps users to determine the optimal gene expression analysis pipeline
The Multi-Pipeline Gene Expression Analysis tool was developed as a prototype during the Bioinformatics Integration Support Contract (BISC) in 2010-2011. It was available online at the ImmPort website in an "Alpha" release until November 2013. The tool utilizes about 300 gene expression analysis pipelines with combinations of methods for: 1. Background Correction (none, mas5, rma, DFCM, RMA-mean, RMA-75) 2. Normalization (none, constant, contrasts, quantiles, invariant set, loess) 3... -
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Bayesian Estimated Core Genome
A pipeline for estimating the core genome of a set of genome sequences
This collection of tools, Bayesian Estimated Core Genome Tools, is intended to provide a simple pipeline for calculating the estimated core genome of a set of genome sequences, based on the output obtained from Genome Comparator [1]. As well as calculating the estimated core genome, tools are also provided for the calculation of median pairwise distances for alignments generated by Genome Comparator for each gene based on the reference genome. Finally, there is a tool for generating...