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.

Varclus – Detection of Positive Selection in Genes and Genomes through Variation Clusters

Varclus

:: DESCRIPTION

Varclus is a perl utility to identify clusters of amino acid or nucleotide changes in a sequence that are too tightly spaced to have occurred by chance alone.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

 Varclus

:: MORE INFORMATION

Citation:

Wagner, A. (2007)
Rapid detection of positive selection in genes and genomes through variation clusters.
Genetics 176: 2451–2463

CoRe v1.0.2 – Identifying Core-fitness Genes in Genome-wide Pooled CRISPR-Cas9 Screens

CoRe v1.0.2

:: DESCRIPTION

CoRe is an R package implementing existing and novel methods for the identification of core-fitness genes (at two different level of stringency) from joint analyses of multiple CRISPR-Cas9 screens.

::DEVELOPER

CoRe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

CoRe

:: MORE INFORMATION

Citation

Vinceti A, Karakoc E, Pacini C, Perron U, De Lucia RR, Garnett MJ, Iorio F.
CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens.
BMC Genomics. 2021 Nov 17;22(1):828. doi: 10.1186/s12864-021-08129-5. PMID: 34789150.

MaxTiC – Ranking Nodes in a Phylogeny using inferred Horizontal Gene Transfers

MaxTiC

:: DESCRIPTION

MaxTiC (Maximum Time Consistency) is a software which takes as input a species tree and a series of (possibly inconsistent) time constraints between its internal nodes, weighted by confidence scores.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MaxTiC

:: MORE INFORMATION

Citation

MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers
Cédric ChauveAkbar RafieyAdrián A. DavínCeline ScornavaccaPhilippe VeberBastien BoussauGergely J. SzöllősiVincent DaubinEric Tannier

PhySca – SCJ small parsimony problem for weighted Gene Adjacencies

PhySca

:: DESCRIPTION

PhySca samples solutions to the Single-Cut-and-Join (SCJ) small parsimony problem for weighted gene adjacencies.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PhySca

:: MORE INFORMATION

Citation

Luhmann N, Lafond M, Thevenin A, Ouangraoua A, Wittler R, Chauve C.
The SCJ Small Parsimony Problem for Weighted Gene Adjacencies.
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1364-1373. doi: 10.1109/TCBB.2017.2661761. Epub 2017 Jan 31. PMID: 28166504.

ANGST – ANalyzer of Gene and Species Trees

ANGST

:: DESCRIPTION

AnGST performs a phylogenetic reconciliation between a given species and gene tree, positing the best scoring set of HGT, DUP, and LOS events to explain all topological incongruities between the two trees. In order to protect against phylogenetic noise, we have designed AnGST to be capable of incorporating information from dozens of bootstrap trees simultaneously. In cases of variations among bootstrap subtrees, the subtree that best accords with the reference tree is adopted.

::DEVELOPER

The Alm lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

 ANGST

:: MORE INFORMATION

Citation

LA David & EJ Alm.
Rapid evolutionary innovation during an Archaean Genetic Expansion.”
Nature, 2010. doi:10.1038/nature09649.

GeneSelector 1.0 – Find Small subset of Genes for Classification of Expression data

GeneSelector 1.0

:: DESCRIPTION

GeneSelector finds a small subset of genes for classification of expression data.

::DEVELOPER

Ari Frank. @Laboratory of Computational Biology , Technion

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GeneSelector

:: MORE INFORMATION

RAP – Rank Aggregation-based data Fusion for Gene Prioritization

RAP

:: DESCRIPTION

RAP is a rank aggregation-based data fusion approach for gene prioritization in plants. It can be used to perform the gene prioritization in Arabidopsis thaliana and 28 non-plant species.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

RAP

:: MORE INFORMATION

Citation

Zhai J, Tang Y, Yuan H, Wang L, Shang H, Ma C.
A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function.
Front Plant Sci. 2016 Dec 15;7:1914. doi: 10.3389/fpls.2016.01914. PMID: 28018423; PMCID: PMC5156684.

TAGOPSIN 1.3 – Collating Taxa-specific Gene and Protein Functional and Structural Information

TAGOPSIN 1.3

:: DESCRIPTION

TAGOPSIN (TAxonomy, Gene, Ontology, Protein, Structure INtegrated) retrieves select data from NCBI Taxonomy, NCBI Nucleotide, UniProtKB, Gene Ontology, Pfam, EBI SIFTS and RCSB PDB, and assembles them in the database management system PostgreSQL. TAGOPSIN is an organism-centred data warehousing tool that works with prokaryotic and eukaryotic organisms as well as viruses.

::DEVELOPER

TAGOPSIN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java
  • PostgreSQL

:: DOWNLOAD

TAGOPSIN

:: MORE INFORMATION

Citation

Bundhoo E, Ghoorah AW, Jaufeerally-Fakim Y.
TAGOPSIN: collating taxa-specific gene and protein functional and structural information.
BMC Bioinformatics. 2021 Oct 23;22(1):517. doi: 10.1186/s12859-021-04429-5. PMID: 34688246; PMCID: PMC8541804.

DigSee v2.01 – Disease Gene Search Engine with Evidence Sentence

DigSee v2.01

:: DESCRIPTION

DigSee is a text mining search engine to provide evidence sentences describing that “genes” are involved in the development of “disease” through “biological events”. Biological events such as gene expression, regulation, phosphorylation, localization, and protein catabolism play important roles in the development of diseases. Understanding the association between diseases and genes can be enhanced with the identification of involved biological events in this association. With input of (disease, genes, events), users can obtain Medline abstracts with highlighted evidence sentences.

::DEVELOPER

Data Mining & Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Kim J, So S, Lee HJ, Park JC, Kim JJ, Lee H.
DigSee: Disease gene search engine with evidence sentences (version cancer).
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W510-7. doi: 10.1093/nar/gkt531. Epub 2013 Jun 12. PMID: 23761452; PMCID: PMC3692119.