EPIG-Seq v1.0 – Extracting Patterns and Identifying co-expressed Genes from RNA-Seq

EPIG-Seq v1.0

:: DESCRIPTION

EPIG-Seq is an algorithm and software to identify gene expression patterns from RNA-Seq count data. Once the patterns are identified, co-expressed genes are clustered to the patterns.

::DEVELOPER

EPIG-Seq team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

EPIG-Seq

:: MORE INFORMATION

Citation:

BMC Genomics. 2016 Mar 22;17:255. doi: 10.1186/s12864-016-2584-7.
EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data.
Li J, Bushel PR.

VLASPD – Discovering Variable-Length Patterns in Protein Sequences for PPI Prediction

VLASPD

:: DESCRIPTION

VLASPD considers variable-length segments in protein sequences for protein-protein Interaction prediction

::DEVELOPER

Allen, Lun Hu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

 VLASPD

:: MORE INFORMATION

Citation

IEEE Trans Nanobioscience. 2015 May 21
Discovering Variable-Length Patterns in Protein Sequences for Protein-Protein Interaction Prediction.
Hu L, Chan K.

NGlycPred – N-linked Glycosylation Prediction Server Incorporating Structural Information and Patterns

NGlycPred

:: DESCRIPTION

NGlycPred predicts the glycan occupancy of N-X-T/S sequons of eukaryotic proteins.

::DEVELOPER

Vaccine Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2249-55. doi: 10.1093/bioinformatics/bts426. Epub 2012 Jul 10.
Computational prediction of N-linked glycosylation incorporating structural properties and patterns.
Chuang GY1, Boyington JC, Joyce MG, Zhu J, Nabel GJ, Kwong PD, Georgiev I.

GREVE – Identification of Patterns across Individual Cancer Samples

GREVE

:: DESCRIPTION

GREVE (Genomic Recurrent Event ViEwer) has been developed to assist with the identification of recurrent genomic aberrations across cancer samples.

::DEVELOPER

Jean-Baptiste Cazier

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 GREVE

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2981-2. doi: 10.1093/bioinformatics/bts547. Epub 2012 Sep 8.
GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples.
Cazier JB1, Holmes CC, Broxholme J

LocalDiff 201309 – Characterize Non-stationary Patterns of Isolation by Distance

LocalDiff 201309

:: DESCRIPTION

LocalDiff provides Bayesian measures of Local Genetic Differentiation to characterize non-stationary patterns of isolation by distance.

::DEVELOPER

Nicolas Duforet-Frebourg and Michael Blum

:: SCREENSHOTS

LocalDiff

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 LocalDiff

:: MORE INFORMATION

Citation

Non-stationary patterns of isolation-by-distance: inferring measures of genetic Friction.
Nicolas Duforet-Frebourg, Michael G. B. Blum.
arXiv:1209.5242