Tag: Analysis Toolkit

Metafast v1.0.0 – METAgenome FAST Analysis Toolkit

Metafast v1.0.0

:: DESCRIPTION

Metafast is a tool for fast graph-based reference-free comparison of shotgun metagenomic data.

::DEVELOPER

Computer Technologies Laboratory, National Research University of Information Technologies,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOs
  • Java
:: DOWNLOAD

Metafast

:: MORE INFORMATION

Citation

Ulyantsev VI, Kazakov SV, Dubinkina VB, Tyakht AV, Alexeev DG.
MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data.
Bioinformatics. 2016 Sep 15;32(18):2760-7. doi: 10.1093/bioinformatics/btw312. Epub 2016 Jun 3. PMID: 27259541.

Triplex-Inspector 0.1.3 – Triplex Target Analysis Toolkit

Triplex-Inspector 0.1.3

:: DESCRIPTION

Triplex-Inspector is a software pipeline based on Triplexator, which enables the screening of genomic sequences for sites that can be targeted by triplex-forming molecules.

::DEVELOPER

Triplex-Inspector team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Python
  • BioPython
  • BEDtools

:: DOWNLOAD

 Triplex-Inspector

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1895-7. doi: 10.1093/bioinformatics/btt315.
Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci.
Buske FA, Bauer DC, Mattick JS, Bailey TL.

PATO v1.0.2 – Pangenome Analysis Toolkit

PATO v1.0.2

:: DESCRIPTION

PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species. It allows to analyze the core-genome, accessory genome and whole genome, the population structure, and the horizontal gene transfer dynamics.

:: DEVELOPER

irycis Bioinfo

:: REQUIREMENTS

  • Linux / Window
  • R

:: DOWNLOAD

PATO

:: MORE INFORMATION

Citation

Fernández-de-Bobadilla MD, Talavera-Rodríguez A, Chacón L, Baquero F, Coque TM, Lanza VF.
PATO: Pangenome Analysis Toolkit.
Bioinformatics. 2021 Oct 8:btab697. doi: 10.1093/bioinformatics/btab697. Epub ahead of print. PMID: 34623430.

EBImage 4.35.0 – Image Processing and Analysis Toolkit for R

EBImage 4.35.0

:: DESCRIPTION

EBImage provides general purpose functionality for reading, writing, processing and analysis of images. Furthermore, in the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 EBImage

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Apr 1;26(7):979-81. doi: 10.1093/bioinformatics/btq046.
EBImage–an R package for image processing with applications to cellular phenotypes.
Pau G, Fuchs F, Sklyar O, Boutros M, Huber W.

BEAT 1.31.0 – BS-Seq Epimutation Analysis Toolkit

BEAT 1.31.0

:: DESCRIPTION

BEAT implements all bioinformatics steps required for the quantitative high-resolution analysis of DNA methylation patterns from bisulfite sequencing data, including the detection of regional epimutation events, i.e. loss or gain of DNA methylation at CG positions relative to a reference.

::DEVELOPER

Single Cell Omics Germany

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 BEAT

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 27. [Epub ahead of print]
Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data.
Akman K1, Haaf T, Gravina S, Vijg J, Tresch A.

WebGestalt 2019 – WEB-based GEne SeT AnaLysis Toolkit

WebGestalt 2019

:: DESCRIPTION

WebGestalt is designed for functional genomic, proteomic and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides an easy way for biologists to make sense out of gene lists.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W77-83. doi: 10.1093/nar/gkt439. Epub 2013 May 23.
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013.
Wang J1, Duncan D, Shi Z, Zhang B.

KAT 2.4.2 – K-mer Analysis Toolkit

KAT 2.4.2

:: DESCRIPTION

KAT is a suite of tools that generate, analyse and compare k-mer spectra produced from sequence files.

::DEVELOPER

the Earlham Institute

:: SCREENSHOTS

N/a

:: REQUIREMENTS

:: DOWNLOAD

 KAT

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 15;33(4):574-576. doi: 10.1093/bioinformatics/btw663.
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.
Mapleson D, Garcia Accinelli G, Kettleborough G, Wright J, Clavijo BJ.