iLocator – An Image-based Multi-label Human Protein Subcellular Localization Predictor

iLocator

:: DESCRIPTION

iLocator is an image-based multi-label subcellular location predictor, which covers 7 cellular localizations, i.e. cytoplasm, endoplasmic reticulum, Golgi apparatus, lysosome, mitochondria, nucleus, and vesicles. The iLocator incorporates both global and local image descriptors, and uses an ensemble multi-label classifier to generate accurate predictions.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

iLocator

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 iLocator

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Aug 15;29(16):2032-40. doi: 10.1093/bioinformatics/btt320. Epub 2013 Jun 4.
An image-based multi-label human protein subcellular localization predictor (iLocator) reveals protein mislocalizations in cancer tissues.
Xu YY1, Yang F, Zhang Y, Shen HB.

FuncEpiMod 2.7 – Identification of Functional Epigenetic Modules (FEM)

FuncEpiMod 2.7

:: DESCRIPTION

FuncEpiMod (Functional Epigenetic Modules ,FEM) is a novel functional supervised algorithm for the integrative analysis of Infinium 450k DNA methylation and matched or unmatched gene expression data.

::DEVELOPER

FuncEpiMod team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 FuncEpiMod

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 2. [Epub ahead of print]
A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control.
Jiao Y1, Widschwendter M, Teschendorff AE.

LogMiNeR 0.1.0 – Logistic Multiple Network-constrained Regression

LogMiNeR 0.1.0

:: DESCRIPTION

LogMiNeR is a method for analyzing high-throughput transcriptional profiling data (e.g., microarray or RNA-seq) in which multiple networks encoding prior knowledge are incorporated within a logistic modeling framework to improve model interpretability.

::DEVELOPER

Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

LogMiNeR

:: MORE INFORMATION

Citation

Avey S, et al.
Multiple network-constrained regressions expand insights into influenza vaccination responses.
Bioinformatics,33 (14), i208-i216 2017 Jul 15

TIgGER 0.4.0 – Infers Novel Immunoglobulin Alleles from Sequencing Data

TIgGER 0.4.0

:: DESCRIPTION

TIgGER (Tool for Ig Genotype Elucidation via airR-seq) is a set of methods for identifying novel V gene alleles and constructing subject-specific genotypes.

::DEVELOPER

Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

TIgGER

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A, 112 (8), E862-70 2015 Feb 24
Automated Analysis of High-Throughput B-cell Sequencing Data Reveals a High Frequency of Novel Immunoglobulin V Gene Segment Alleles
Gadala-Maria D, Yaari G, Uduman M, Kleinstein SH.

stAIcalc – tAI Calculator based on Species-specific Weights

stAIcalc

:: DESCRIPTION

stAIcalc is a tAI(tRNA Adaptation Index) Calculator based on a species-specific inference of these weights.

::DEVELOPER

Tamir Tuller’s Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • MatLab

:: DOWNLOAD

stAIcalc

:: MORE INFORMATION

Citation

stAIcalc: tRNA adaptation index calculator based on species-specific weights.
Sabi R, Volvovitch Daniel R, Tuller T.
Bioinformatics. 2017 Feb 15;33(4):589-591. doi: 10.1093/bioinformatics/btw647.

ChimeraUGEM 1.01 – Unsupervised Gene Expression Modeling in any given Organism

ChimeraUGEM 1.01

:: DESCRIPTION

ChimeraUGEM provides tools for the analysis of gene sequences (coding and non-coding), as well as the design of protein coding sequences for optimized expression, based on the Chimera algorithms and codon usage optimization.

::DEVELOPER

Tamir Tuller’s Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • MatLab

:: DOWNLOAD

ChimeraUGEM

:: MORE INFORMATION

Citation

Diament et al.
ChimeraUGEM: unsupervised gene expression modeling in any given organism.
Bioinformatics, 35 (18), 3365-3371 2019 Sep 15

RFMapp 20121217 – Ribosome Flow Model Application

RFMapp 20121217

:: DESCRIPTION

The RFMapp is a graphical user interface application, enabling the prediction of fundamental features of the gene translation process, including translation rates, ribosomal densities, protein abundance levels, and the relation between all these variables.

::DEVELOPER

Tamir Tuller’s Group

:: SCREENSHOTS

RFMapp

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 RFMapp

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 15;28(12):1663-4. doi: 10.1093/bioinformatics/bts185. Epub 2012 Apr 11.
RFMapp: ribosome flow model application.
Zur H1, Tuller T.

piMGM 1.0 – Mixed Graphical Model with Prior Information

piMGM 1.0

:: DESCRIPTION

piMGM is a new method, which can learn with accuracy the structure of probabilistic graphs over mixed data by appropriately incorporating priors from multiple experts with different degrees of reliability.

:: DEVELOPER

Benos Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

piMGM

:: MORE INFORMATION

Citation:

Bioinformatics, 34 (17), i848-i856 2018 Sep 1
piMGM: Incorporating Multi-Source Priors in Mixed Graphical Models for Learning Disease Networks
Dimitris V Manatakis , Vineet K Raghu , Panayiotis V Benos

ssNPA 1.0 – subtyping samples based on Deregulation of their Gene Networks

ssNPA 1.0

:: DESCRIPTION

ssNPA is a new approach for subtyping samples based on deregulation of their gene networks.

:: DEVELOPER

Benos Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ssNPA

:: MORE INFORMATION

Citation:

Bioinformatics 2019 Dec 24[Online ahead of print]
Causal Network Perturbations for Instance-Specific Analysis of Single Cell and Disease Samples
Kristina L Buschur , Maria Chikina , Panayiotis V Benos