:: DESCRIPTION
CREEDS is a portal for visualizing and querying the collections of the gene expression signatures.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nat Commun. 2016 Sep 26;7:12846. doi: 10.1038/ncomms12846.
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.
Wang Z etc.
:: DESCRIPTION
ARCHS4 is a web resource that makes the majority of published RNA-seq data from human and mouse available at the gene and transcript levels.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nat Commun. 2018 Apr 10;9(1):1366. doi: 10.1038/s41467-018-03751-6.
Massive mining of publicly available RNA-seq data from human and mouse.
Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma’ayan A.
:: DESCRIPTION
Genefu contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.
::DEVELOPER
Princess Margaret Bioinformatics and Computational Genomics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.
Gendoo DM, Ratanasirigulchai N, Schröder MS, Paré L, Parker JS, Prat A, Haibe-Kains B.
Bioinformatics. 2015 Nov 24. pii: btv693.
:: DESCRIPTION
SCUDO (Signature-based ClUstering for DiagnOstic purposes) is a tool for clustering gene expression profiles for diagnostic purposes using a new type of rank-based signatures
::DEVELOPER
The Microsoft Research – University of Trento Centre for Computational and Systems Biology
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
SCUDO: a tool for signature-based clustering of expression profiles.
Lauria M, Moyseos P, Priami C.
Nucleic Acids Res. 2015 May 9. pii: gkv449.
:: DESCRIPTION
MetaProb is a novel assembly-assisted tool for unsupervised metagenomic binning.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics, 32 (17), i567-i575 2016 Sep 1
MetaProb: Accurate Metagenomic Reads Binning Based on Probabilistic Sequence Signatures
Samuele Girotto 1, Cinzia Pizzi 1, Matteo Comin 1
:: DESCRIPTION
MARQ (Microarray Rank Query) is an online microarray retrieval tool based on rank statistics. Datasets in MARQ, most of them retrieved from GEO, are processed into signatures, which are lists of genes ranked by their level of differential expression. Each dataset defines one of more of these signatures based on the possible comparisons of its constituent samples.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
No
:: MORE INFORMATION
Citation
Vazquez, M., Nogales-Cadenas, R., Arroyo, J., Botías, P., García, R., Carazo, J. M., Tirado, F., Pascual-Montano, A. Carmona-Saez, P. 2010,
`MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures.’ ,
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W228-32.
:: DESCRIPTION
ChAT (Chromatin-profile Alignment followed by Tree-clustering algorithm) employs dynamic programming of combinatorial histone modification profiles to identify locally similar chromatin sub-regions and provides complementary utility with respect to existing methods.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2012 Nov;40(21):10642-56. doi: 10.1093/nar/gks848. Epub 2012 Sep 18.
Chromatin signature discovery via histone modification profile alignments.
Wang J, Lunyak VV, Jordan IK.
:: DESCRIPTION
ChromaSig is an unsupervised learning method, which finds, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gary Hon, Bing Ren, Wei Wang
ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome
PLoS Comput Biol 4(10): e1000201.
