LOX 1.8beta – Inferring Level of Expression from Diverse Methods of Census Sequencing

LOX 1.8beta

:: DESCRIPTION

LOX (Level Of eXpression) is a program that employs Markov Chain Monte Carlo to estimate level of expression from census sequencing data sets with multiple treatments or samples.

::DEVELOPER

the Townsend Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++Compiler

:: DOWNLOAD

 LOX

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Aug 1;26(15):1918-9. Epub 2010 Jun 10.
LOX: inferring Level Of eXpression from diverse methods of census sequencing.
Zhang Z, López-Giráldez F, Townsend JP.

MADE 20110209 – Metabolic Adjustment by Differential Expression

MADE 20110209

:: DESCRIPTION

MADE uses the statistical significance of changes in gene or protein expression to create a functional metabolic model that most accurately recapitulates the expression dynamics.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 MADE

:: MORE INFORMATION

Citation:

Jensen, P.A. and J.A. Papin. 2011.
Functional integration of a metabolic network model and expression data without arbitrary thresholding.
Bioinformatics, 27(4):541-547.

TIGER 1.2.0-beta – Toolbox for Integrating Genome-scale metabolism, Expression, and Regulation

TIGER 1.2.0-beta

:: DESCRIPTION

TIGER is a software platform for building and analyzing genome-scale models of metabolism. TIGER provides methods for combining gene-protein-reaction associations, transcriptional regulation, and other biological constraints into a single mixed-integer linear programming (MILP) framework.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab
:: DOWNLOAD

 TIGER

:: MORE INFORMATION

Citation

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.
Jensen PA, Lutz KA, Papin JA.
BMC Syst Biol. 2011 Sep 23;5:147. doi: 10.1186/1752-0509-5-147.

CIBERSORTx / CIBERSORT – Determining Cell Type Abundance and Expression from Bulk Tissues

CIBERSORTx / CIBERSORT

:: DESCRIPTION

CIBERSORTx is an analytical tool to impute gene expression profiles and provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data.

CIBERSORT is an analytical tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data.

::DEVELOPER

Newman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Determining cell type abundance and expression from bulk tissues with digital cytometry
Newman AM, et al.
Nat Biotechnol, 37 (7), 773-782 Jul 2019

CytoTRACE beta – Cellular (Cyto) Trajectory Reconstruction Analysis using gene Counts and Expression

CytoTRACE beta

:: 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

Newman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

CytoTRACE

:: 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.

SCUDO – Signature-based Clustering of Expression Profiles

SCUDO

:: 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

  • Web browser

:: 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.

DANCE 0.99.0 – Deregulation of Copy-number and Expression

DANCE 0.99.0

:: DESCRIPTION

DANCE quantifies the impact of copy-number alterations on gene expression and compares it between tumour sub-types.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

 DANCE

:: 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.

CSTP 1.0 – Condition-specific Target Prediction from Motifs and Expression

CSTP 1.0

:: 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

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 27
Condition-specific target prediction from motifs and expression.
Meng G1, Vingron M.

canEvolve – Integrative Cancer Genomics analysis of Expression, Copy Number, miRNAs and Network

canEvolve

:: DESCRIPTION

canEvolve query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. canEvolve stores gene, microRNA (miRNA) and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information. canEvolve allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. At present canEvolve provides different types of information extracted from 90 cancer genomics studies comprising of more than 10,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network analysis and ability to query gene lists/pathways are distinctive features of canEvolve. canEvolve will facilitate integrative and meta-analysis of oncogenomics datasets.

::DEVELOPER

CanEvolve Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

canEvolve: a web portal for integrative oncogenomics.
Samur MK, Yan Z, Wang X, Cao Q, Munshi NC, Li C, Shah PK.
PLoS One. 2013;8(2):e56228. doi: 10.1371/journal.pone.0056228.

DICER – Differential Correlation in Expression for meta-module Recovery

DICER

:: DESCRIPTION

DICER is a tool for advanced analysis of differential co-expression (DC) case-control gene expression data.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • Java 

:: DOWNLOAD

 DICER

:: 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.