:: DESCRIPTION
CytoTRACE is a computational method to predict the differentiation states of cells from single-cell RNA-sequencing data, without prior knowledge of developmental orderings
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Science, 367 (6476), 405-411 2020 Jan 24
Single-cell Transcriptional Diversity Is a Hallmark of Developmental Potential
Gunsagar S Gulati et al.
:: 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
:: 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
DANCE quantifies the impact of copy-number alterations on gene expression and compares it between tumour sub-types.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Oct 1;27(19):2679-85. doi: 10.1093/bioinformatics/btr450. Epub 2011 Jul 30.
Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer.
Yuan Y1, Rueda OM, Curtis C, Markowetz F.
:: DESCRIPTION
CSTP is a computational tool to predict the TF-target regulation with expression data based on a philosophy of guilt by association. Different from other tools, CSTP does not insist on clear TF binding site in the promoters of target genes.The expression information of genes allows prediction of CSTP to be condition-specific or tissue-specific
::DEVELOPER
Department Computational Molecular Biology, Max Planck Institute for Molecular Genetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Feb 27
Condition-specific target prediction from motifs and expression.
Meng G1, Vingron M.
:: DESCRIPTION
DICER is a tool for advanced analysis of differential co-expression (DC) case-control gene expression data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS Comput Biol. 2013;9(3):e1002955. doi: 10.1371/journal.pcbi.1002955. Epub 2013 Mar 7.
Dissection of regulatory networks that are altered in disease via differential co-expression.
Amar D1, Safer H, Shamir R.
:: DESCRIPTION
DEXUS identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions.
::DEVELOPER
Institute of Bioinformatics, Johannes Kepler University Linz
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2013 Nov;41(21):e198. doi: 10.1093/nar/gkt834. Epub 2013 Sep 17.
DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions.
Klambauer G1, Unterthiner T, Hochreiter S.
:: DESCRIPTION
ProMISe is a novel approach to infer Probabilistic MiRNA-mRNA Interaction Signature from a single pair of miRNA-mRNA expression profile. Our model considers mRNA and miRNA competition as a probabilistic function of the expressed seeds (matches).
::DEVELOPER
Yue Li @ The Zhang Lab, University of Toronto
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Li, Y., Liang, C., Wong, KC, Jin, K., and Zhang, Z. (Feb, 2014)
Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach. Nucleic Acids Research
Nucl. Acids Res. (2014) doi: 10.1093/nar/gku182
:: DESCRIPTION
NLDMseq is a bioinformatics tool for expression calculation at both gene and isoform levels from RNA-seq data by considering isoform- and exon-specific read sequencing rate.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.
Liu X, Shi X, Chen C, Zhang L.
BMC Bioinformatics. 2015 Oct 16;16(1):332. doi: 10.1186/s12859-015-0750-6.
:: DESCRIPTION
E-miR is an easy to use perl-based analysis pipeline which was developed to handle the sequencing data in several automated steps including data format conversion, 3′ adapter removal, genome alignment and annotation to non-coding RNA transcripts.
::DEVELOPER
Leiden Genome Technology Center
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Genomics. 2010 Dec 20;11:716. doi: 10.1186/1471-2164-11-716.
New methods for next generation sequencing based microRNA expression profiling.
Buermans HP, Ariyurek Y, van Ommen G, den Dunnen JT, ‘t Hoen PA.
:: DESCRIPTION
pPIC9 is a program for evaluation and design for high-level expression of foreign genes in pPIC9 vector
::DEVELOPER
Center of Computational Biology, Beijing Institute of Basic Medical Sciences
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Construction of mathematical model for high-level expression of foreign genes in pPIC9 vector and its verification.
Wu B, Cha L, Du Z, Ying X, Li H, Xu L, Zheng X, Li E, Li W.
Biochem Biophys Res Commun. 2007 Mar 9;354(2):498-504
