LPIA v1 – Latent Pathway Identification Analysis

LPIA v1

:: DESCRIPTION

LPIA is a computational method for identifying biological pathways as putative sources of transcriptional dysregulation. It looks for statistically signficant evidence of dysregulation in a network of pathways constructed in a manner that explicitly links pathways through their common function in the cell.

::DEVELOPER

Eric D. Kolaczyk

:: SCREENSHOTS

n/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 LPIA

:: MORE INFORMATION

Citation

Pham, L., Christadore, L., Schaus, S., and Kolaczyk, E.D. (2011).
Network-based prediction for sources of transcriptional dysregulation via latent pathway identification analysis.
Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1100891108.

SAMMate 2.7.4 / assemblySAM 1.1 – Processing Short Read Alignments in SAM/BAM format / RNA-Seq Assembly and Analysis

SAMMate 2.7.4 / assemblySAM 1.1

:: DESCRIPTION

SAMMate is an open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

assemblySAM employs a novel method to localize and assemble RNA-seq reads into RNA transcript sequences.

::DEVELOPER

Dongxiao Zhu, Ph.D

:: SCREENSHOTS

sammate

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java
  • R package

:: DOWNLOAD

 SAMMate / assemblySAM

:: MORE INFORMATION

Citation:

Source Code Biol Med. 2011 Jan 13;6(1):2. doi: 10.1186/1751-0473-6-2.
SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.
Xu G1, Deng N, Zhao Z, Judeh T, Flemington E, Zhu D.

Nguyen, T, Zhao, Z, Zhu, D.
SPATA: A seeding and patching algorithm for hybrid transcriptome assembly.

Nguyen, T, Deng, N, Zhu, D.
SASeq: A selective and adaptive shrinkage approach to detect and quantify active transcripts using RNA-Seq.

BIANA 1.4.5 – Biologic Interaction and Network Analysis

BIANA 1.4.5

:: DESCRIPTION

BIANA (Biologic Interactions and Network Analysis) is a biological database integration and network management framework written in Python. It uses a high level abstraction schema to define databases providing any kind of biological information (both individual entries and their relationships).

::DEVELOPER

Structural BioInformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BIANA

:: MORE INFORMATION

Citation

Biana: a software framework for compiling biological interactions and analyzing networks.
Garcia-Garcia J, Guney E, Aragues R, Planas-Iglesias J, Oliva B.
BMC Bioinformatics. 2010 Jan 27;11:56.

ANAT 20180308 – Inference and Analysis of Functional Networks of Proteins

ANAT 20180308

:: DESCRIPTION

ANAT (Advanced Network Analysis Tool) , is an all-in-one resource that provides access to up-to-date large-scale physical association data in several organisms, advanced algorithms for network reconstruction, and a number of tools for exploring and evaluating the obtained network models

::DEVELOPER

Prof. Roded Sharan

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ANAT

:: MORE INFORMATION

Citation

ANAT: A Tool for Constructing and Analyzing Functional Protein Networks.
N. Yosef, E. Zalckvar, A. D. Rubinstein, M. Homilius, N. Atias, L. Vardi, I. Berman, H. Zur, A. Kimchi, E. Ruppin and R. Sharan
Sci. Signal. 4, pl1 (2011).

GSDCA – Gene Set Differential Coordination Analysis

GSDCA

:: DESCRIPTION

GSDCA finds gene sets that are differentially coordinated with the rest of the genome between treatment conditions. It also finds differentially coordinated gene set pairs.

::DEVELOPER

Tianwei Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

GSDCA

:: MORE INFORMATION

Citation

Genomics. 2011 Dec;98(6):469-77. doi: 10.1016/j.ygeno.2011.09.001.
Capturing changes in gene expression dynamics by gene set differential coordination analysis.
Yu T, Bai Y.

EXPANDER 7.2 – Gene Expression Analysis & Visualization

EXPANDER 7.2

:: DESCRIPTION

EXPANDER (EXpression Analyzer and DisplayER) is a java-based tool for analysis of gene expression data.It is capable of (1) preprocessing (2) visualizing (3) clustering (4) biclustering and (5) performing downstream analysis of clusters and biclusters such as functional enrichment and promoter analysis It seamlessly integrates in one package all analysis steps, including:

  • Data preprocessing and normalization
  • Identification of differential genes
  • Clustering and biclustering;
  • Down-stream enrichment analyses of:
    – GO functional categories
    – TF binding sites in promoter regions
    – MicroRNA sites in 3′-UTRs and
    – Chromosomal locations
  • Network-based analysis of the expression data.

EXPANDER provides support for analysis of human, mouse, rat, chicken, fly, zebrafish, C. elegans, yeast (s.cerevisiaeand s. pombe), arabidopsis, tomato, listeria, A. fumigatus and E. coli.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

EXPANDER

:: MORE INFORMATION

Citation

Expander: from expression microarrays to networks and functions.
Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R.
Nat Protoc. 2010 Feb;5(2):303-22. doi: 10.1038/nprot.2009.230.

Imaris 9.3.1 – Analysis, Segmentation and Interpretation of 3D and 4D Microscopy datasets

Imaris 9.3.1

:: DESCRIPTION

Imaris is a scientific software module for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets.

::DEVELOPER

Imaris team

:: SCREENSHOTS

Imaris

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

 Imaris

:: MORE INFORMATION

VANTED 2.6.5 – Visualization and Analysis of Networks containing Experimental Data

VANTED 2.6.5

:: DESCRIPTION

VANTED (Visualisation and Analysis of Networks containing Experimental Data) is an open source software that offers the possibility to load and edit graphs, which may represent biological pathways or functional hierarchies. It allows to integrate different *omics data into the functional context and provides a variety of functions for data mapping and processing, statistical analysis, and visualisation. With the VANTED Add-on interface it is easily possible to extend the functionality of the software.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 VANTED

:: MORE INFORMATION

Citation

Klukas and Schreiber (2010)
Integration of -omics data and networks for biomedical research with VANTED.
Journal of Integrative Biology, 7(2)

Björn H. Junker, Christian Klukas and Falk Schreiber (2006)
VANTED: A system for advanced data analysis and visualization in the context of biological networks.
BMC Bioinformatics, 7:109

RNAcode 0.3 – Analysis of Protein Coding Potential in Multiple Sequence Alignments

RNAcode 0.3

:: DESCRIPTION

RNAcode predicts protein coding regions in a a set of homologous nucleotide sequences. RNAcode relies on evolutionary signatures including synonymous/conservative mutations and conservation of the reading frame. It does not use any species specific sequence characteristics whatsoever and does not use any machine learning techniques.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAcode

:: MORE INFORMATION

Citation:

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.
RNA. 2011;17(4):578-94.

ZoomX 1.0.0 – Single Molecule Based Rearrangement Analysis with Linked Read Sequencing

ZoomX 1.0.0

:: DESCRIPTION

ZoomX analyzes single molecule whole genome sequencing data sets to identify long-range rearrangements.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

ZoomX

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2018 Feb 28;46(4):e19. doi: 10.1093/nar/gkx1193.
Identification of large rearrangements in cancer genomes with barcode linked reads.
Xia LC, Bell JM, Wood-Bouwens C, Chen JJ, Zhang NR, Ji HP.