LOLA 1.24.0 / LOLAweb – Genomic Locus Overlap Enrichment Analysis

LOLA 1.24.0 / LOLAweb

:: DESCRIPTION

LOLA (Locus Overlap Analysis) is an R Bioconductor package for genomic locus overlap enrichment. LOLA lets you test your genomic ranges of interest against a database of other genomic range sets to identify enrichment of overlap, tying external annotation to your regions of interest.

LOLAweb is server with public hosting of our shiny interface to the LOLA R-package.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 LOLA

:: MORE INFORMATION

Citation

Nagraj VP, Magee NE, Sheffield NC.
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.
Nucleic Acids Res. 2018 Jul 2;46(W1):W194-W199. doi: 10.1093/nar/gky464. PMID: 29878235; PMCID: PMC6030814.

LOLA: Enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.
Sheffield NC, Bock C.
Bioinformatics. 2015 Oct 27. pii: btv612.

MGEnrichment – Microglia Gene List Enrichment Calculator

MGEnrichment

:: DESCRIPTION

MGEnrichment is a web application developed both to disseminate to the community our curated database of microglia-relevant gene lists, and to allow non-programming scientists to easily conduct statistical enrichment analysis on their gene expression data.

::DEVELOPER

Ciernia Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server

:: DOWNLOAD

MGEnrichment

:: MORE INFORMATION

Citation

Jao J, Ciernia AV.
MGEnrichment: A web application for microglia gene list enrichment analysis.
PLoS Comput Biol. 2021 Nov 17;17(11):e1009160. doi: 10.1371/journal.pcbi.1009160. PMID: 34788279; PMCID: PMC8598070.

PEGS 0.6.4 – Peak-set Enrichment of Gene-Sets

PEGS 0.6.4

:: DESCRIPTION

PEGS is a Python bioinformatics utility for calculating enrichments of gene clusters at different genomic distances from peaks.

::DEVELOPER

Bioinformatics Core Facility in the Faculty of Biology Medicine and Health at the University of Manchester

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

PEGS

:: MORE INFORMATION

Citation

Briggs P, Hunter AL, Yang SH, Sharrocks AD, Iqbal M.
PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals.
F1000Res. 2021 Jul 15;10:570. doi: 10.12688/f1000research.53926.2. PMID: 34504687; PMCID: PMC8406447.

MAGENTA 2.4 – Meta-Analysis Gene-set Enrichment of variaNT Associations

MAGENTA 2.4

:: DESCRIPTION

MAGENTA (Meta-Analysis Gene-set Enrichment of variaNT Associations) is a program that tests whether predefined biological processes or gene sets are enriched for genes associated with a complex disease or trait.

:DEVELOPER

the Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Matlab

:: DOWNLOAD

 MAGENTA

:: MORE INFORMATION

Citation

Ayellet V. Segrè, DIAGRAM Consortium, MAGIC investigators, Leif Groop, Vamsi K. Mootha, Mark J. Daly, and David Altshuler (2010).
Common Inherited Variation in Mitochondrial Genes is not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits.
PLoS Genetics Aug 12;6(8). pii: e1001058.

Repeat Enrichment Estimator – Measure Enrichment of Annotated Repeat Types in ChIP-seq data

Repeat Enrichment Estimator

:: DESCRIPTION

Repeat enrichment estimator aims to measure the enrichment of annotated repeat types in ChIP-seq data

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Repeat enrichment estimator

:: MORE INFORMATION

Citation

Daniel S Day, Lovelace J Luquette, Peter J Park and Peter V Kharchenko.
Estimating enrichment of repetitive elements from high-throughput sequence data.
Genome Biology 2010, 11:R69 doi:10.1186/gb-2010-11-6-r69

GenomeRunner 4.0 – Annotation and Enrichment of Next-Gen Sequencing Data

GenomeRunner 4.0

:: DESCRIPTION

GenomeRunner is a tool for automating genome exploration. It performs annotation and enrichment analyses of user-provided genomic regions (SNPs, ChIP-seq binding sites etc.) against >6,000 (human genome) epigenomic features available from the UCSC genome browser.

::DEVELOPER

GenomeRunner team

:: SCREENSHOTS

GenomeRunner

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GenomeRunner

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 1;28(3):419-20. doi: 10.1093/bioinformatics/btr666. Epub 2011 Dec 6.
GenomeRunner: automating genome exploration.
Dozmorov MG1, Cara LR, Giles CB, Wren JD.

VSEAMS 0.1 – Variant Set Enrichment Analysis using Multivariate Sampling

VSEAMS 0.1

:: DESCRIPTION

VSEAMS is a pipeline for investigating whether a set of gene/genomic intervals is enriched for genome wide association study (GWAS) p-values for a particular trait.

::DEVELOPER

MRC Biostatistics Unit

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • linux/ Windows/ MacOsX
  • Perl

:: DOWNLOAD

 VSEAMS

:: MORE INFORMATION

Citation

VSEAMS: A pipeline for variant set enrichment analysis using summary GWAS data identifies IKZF3, BATF and ESRRA as key transcription factors in type 1 diabetes.
Burren OS, Guo H, Wallace C.
Bioinformatics. 2014 Aug 27. pii: btu571.

GGEA / EnrichmentBrowser 2.22.2 – Gene Graph Enrichment Analysis

GGEA / EnrichmentBrowser 2.22.2

:: DESCRIPTION

GGEA is an intuitive method to detect consistently and coherently enriched gene sets, based on prior knowledge derived from directed gene regulatory networks. GGEA comes embedded in the EnrichmentBrowser system, a powerful multi-functional framework for enrichment analysis of gene expression data.

::DEVELOPER

Institute for Bioinformatics, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • R package

:: DOWNLOAD

 GGEA

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 1;27(13):i366-73. doi: 10.1093/bioinformatics/btr228.
From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems.
Geistlinger L, Csaba G, Küffner R, Mulder N, Zimmer R.

GREAT 4.0.4 – Genomic Regions Enrichment of Annotations Tool

GREAT 4.0.4

:: DESCRIPTION

GREAT is a web server to analyze the functional significance of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome.

::DEVELOPER

The Bejerano Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nat Biotechnol. 2010 May;28(5):495-501. doi: 10.1038/nbt.1630. Epub 2010 May 2.
GREAT improves functional interpretation of cis-regulatory regions.
McLean CY1, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G.

JEPETTO 1.3.1 – Java Enrichment of Pathways Extended To Topology

JEPETTO 1.3.1

:: DESCRIPTION

JEPETTO is a Cytoscape 3.x plugin performing integrative human gene set analysis. It identifies functional associations between genes and known cellular pathways, and processes using protein interaction networks and topological analysis.

::DEVELOPER

Interdisciplinary Computing and Complex BioSystems (ICOS) research group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 JEPETTO

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Apr 1;30(7):1029-30. doi: 10.1093/bioinformatics/btt732. Epub 2013 Dec 19.
JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks.
Winterhalter C1, Widera P, Krasnogor N.

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