BioSilicoList1

BioSilicoList

A comprehensive list of available in silico tools for genetics and genomics

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Resources for the analysis of genome-wide gene expression

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*Databases

NCBI GEO http://www.ncbi.nlm.nih.gov/sites/entrez?db=gds&cmd=search&term=

ArrayExpress http://www.ebi.ac.uk/microarray-as/ae/

BioGPS (Symatlas) http://biogps.gnf.org/?referer=symatlas#goto=welcome

Allen Brain Atlas http://brain-map.org/welcome.do;jsessionid=443E521520979E11B7191250398A64C3

Mouse Gene Prediction Database http://mgpd.med.utoronto.ca/

SMRI Online Genomics Database https://www.stanleygenomics.org/

NetAffx http://www.affymetrix.com/analysis/index.affx

Genevestigator https://www.genevestigator.ethz.ch/

GeneSapiens http://www.genesapiens.org/

Microarray Gene Expression Database Society http://www.mged.org

Affycomp II A Benchmark for Affymetrix GeneChip Expression Measures http://rafalab.biostat.jhsph.edu/AFFY2/TABLES.hgu/0.html

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*Servers/Programs

GEPAS http://gepas.bioinfo.cipf.es/

Babelomics http://babelomics.bioinfo.cipf.es/

DAVID http://david.abcc.ncifcrf.gov/summary.jsp

Expression Profiler http://www.ebi.ac.uk/expressionprofiler/

Brain Explorer http://mouse.brain-map.org/brainExplorer/index.html

Gene Set Enrichment Analysis (GSEA) http://www.broad.mit.edu/gsea/index.jsp

Clone/Gene ID Converter http://idconverter.bioinfo.cnio.es/

g:Profiler http://biit.cs.ut.ee/gprofiler/welcome.cgi

ID conversion tool http://david.abcc.ncifcrf.gov/conversion.jsp

Pathway-Express http://vortex.cs.wayne.edu/projects.htm

MTOM http://www.genetics.ucla.edu/labs/horvath/MTOM/

SiPaGene http://www.sipagene.de/sipagene/Find

WebGestalt http://bioinfo.vanderbilt.edu/webgestalt/

NIA Array Analysis http://lgsun.grc.nia.nih.gov/ANOVA/

WebArray http://www.webarraydb.org/webarray/index.html

CARMAweb https://carmaweb.genome.tugraz.at/carma/

oneChannelGUI http://www.bioconductor.org/packages/2.1/bioc/html/oneChannelGUI.html

GeneCruiser http://genecruiser.broad.mit.edu/genecruiser3/

GenePattern http://www.broad.mit.edu/cancer/software/genepattern/

PGE http://homes.esat.kuleuven.be/~bioiuser/pge/

Gene List Venn Diagram http://www.bioinformatics.org/gvenn/

List Sorter http://sites.google.com/site/dmbits/BITS-datamining/utilities/list-sorter

TableButler http://angiogenesis.dkfz.de/oncoexpress/software/tablebutler/

A-MADMAN http://compgen.bio.unipd.it/bioinfo/amadman/

MicroArray Retriever http://grenada.lumc.nl/HumaneGenetica/MaRe/

GeneSelector http://www.bioconductor.org/packages/bioc/vignettes/GeneSelector/inst/doc/GeneSelector.pdf

Available Computational Tools for Meta-analyses of Microarray Studies http://sites.google.com/site/compgensite/meta

Bioconductor Packages http://www.bioconductor.org/packages/release/Software.html (list in Google Docs)