Tag: Toolkit

ScoreGene 1.0 – A Gene Expression Data Analysis toolkit

ScoreGene 1.0

:: DESCRIPTION

ScoreGenes is a data analysis toolkit designed for large sets of gene expressions over various experiments. ScoreGenes includes methods for evaluating data sets, discovering informative genes that are differentially expressed across the classes, classifying the experiments using supervised learning algorithms, and clustering the genes using semi-supervised learning method. This toolkit efficiently handles large data sets.

::DEVELOPER

Nir Friedman’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 ScoreGene

:: MORE INFORMATION

CoolBox 0.3.8 – Jupyter Notebook based Genomic data Visualization toolkit

CoolBox 0.3.8

:: DESCRIPTION

CoolBox is an open-source toolkit for visual analysis of genomics data.

:: DEVELOPER

GangCaoLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Window
  • Python

:: DOWNLOAD

CoolBox

:: MORE INFORMATION

Citation

Xu W, Zhong Q, Lin D, Zuo Y, Dai J, Li G, Cao G.
CoolBox: a flexible toolkit for visual analysis of genomics data.
BMC Bioinformatics. 2021 Oct 10;22(1):489. doi: 10.1186/s12859-021-04408-w. PMID: 34629071.

ChemmineR 3.44.0 – Cheminformatics Toolkit for R

ChemmineR 3.44.0

:: DESCRIPTION

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

 ChemmineR

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Aug 1;24(15):1733-4. doi: 10.1093/bioinformatics/btn307.
ChemmineR: a compound mining framework for R.
Cao Y, Charisi A, Cheng LC, Jiang T, Girke T.

ballaxy – Galaxy-based workflow toolkit for Structural Bioinformatics

ballaxy

:: DESCRIPTION

ballaxy is a workflow framework for structure based computational biology based on the Galaxy workflow engine.

::DEVELOPER

BALL Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Windows
  • Web Server
  • C++ Comipiler

:: DOWNLOAD

 ballaxy

:: MORE INFORMATION

Citation:

ballaxy: web services for structural bioinformatics.
Hildebrandt AK, Stöckel D, Fischer NM, de la Garza L, Krüger J, Nickels S, Röttig M, Schärfe C, Schumann M, Thiel P, Lenhof HP, Kohlbacher O, Hildebrandt A.
Bioinformatics. 2014 Sep 2. pii: btu574.

Victor 1.0 – Virtual Construction Toolkit for Proteins

Victor 1.0

:: DESCRIPTION

The Victor library is an open-source project dedicated to providing tools for analyzing and manipulating protein structures.

::DEVELOPER

Bicomputing Group, University of Padua

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  Victor

:: MORE INFORMATION

Citation:

The Victor C++ Library for Protein Representation and Advanced Manipulation.
Hirsh L, Piovesan D, Giollo M, Ferrari C, Tosatto SC.
Bioinformatics. 2014 Nov 19. pii: btu773

RAmiRNA – Viral mature MicroRNA prediction Toolkit

RAmiRNA

:: DESCRIPTION

RAmiRNA (RAdicalmiRNA detector) is a software to solve the problem of custom development of prediction models for mature miRNAs using support vector machine (SVM) learning.

::DEVELOPER

Indo-Russian Centre for Biotechnology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RAmiRNA

:: MORE INFORMATION

Citation

Bioinformation. 2012;8(12):581-5. doi: 10.6026/97320630008581. Epub 2012 Jun 28.
RAmiRNA: Software suite for generation of SVMbased prediction models of mature miRNAs.
Tyagi V, Prasad CS.

BATS – A Basic Analysis Toolkit for Biological Sequences

BATS

:: DESCRIPTION

BATS consists of a collection of libraries that can be used to run basic sequence analysis tasks. Routines for global alignment (LCS from Fragments, Edit Distance with Gaps), local alignment (approximata string matching with K mismateches or differences), and statistical analysis (Filter, Z-Score and Model Generation ) are included.

::DEVELOPER

Raffaele Giancarlo

:: SCREENSHOTS

BATS2

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • Perl

:: DOWNLOAD

 BATS

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2007 Sep 18;2:10.
A basic analysis toolkit for biological sequences.
Giancarlo R1, Siragusa A, Siragusa E, Utro F.

VEGA ZZ 3.2.1.33 – Molecular Modeling Toolkit

VEGA ZZ 3.2.1.33

:: DESCRIPTION

VEGA ZZ is the evolution of the well known VEGA OpenGL package and includes several new features and enhancements making your research jobs very easy. VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it’s evolved to a complete molecular modelling suite. This software is FREE for non-profit academic uses.

::DEVELOPER

Drug Design Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 VEGA ZZ

:: MORE INFORMATION

Citation

Pedretti A., Villa L., Vistoli G.,
“VEGA – An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script” programming“,
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, Vol. 18, 167-173 (2004).

KAnalyze 2.0.0 – DNA/RNA Sequence K-mer Toolkit

KAnalyze 2.0.0

:: DESCRIPTION

KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers.

::DEVELOPER

Vannberg Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 KAnalyze

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 18.
KAnalyze: A Fast Versatile Pipelined K-mer Toolkit.
Audano P1, Vannberg F.

ePEST 1.0 – ChIP-exo Paired-ends Sequencing Processing Toolkit

ePEST 1.0

:: DESCRIPTION

ePEST leverages on the statistical powerful of r-scan for detecting binding peaks with son-3’-end reads and Chernoff inequality for identifying precise borders with exo-5′-end reads, respectively. The detected borders are further modelled as graphical components and classified into distinct border patterns based on their orientation and spacing.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ePEST

:: MORE INFORMATION

Citation

Ye Z, Chen Z, Sunkel B, Frietze S, Huang TH, Wang Q, Jin VX.
Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1.
Nucleic Acids Res. 2016 Sep 19;44(16):7540-54. doi: 10.1093/nar/gkw659. Epub 2016 Jul 25. PMID: 27458208; PMCID: PMC5027512.