Tag: Processing

SePIA – RNA Sequence Processing, Integration, and Analysis

SePIA

:: DESCRIPTION

SePIA is a comprehensive RNA Sequencing workflow standardizing Processing, Integration, and Analysis of large-scale sequencing data. It provides a systematic, pipeline architecture to manage, individually analyze, and integrate both small-RNA and RNA data.

::DEVELOPER

Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SePIA

:: MORE INFORMATION

Citation

SePIA: RNA and small RNA sequence processing, integration, and analysis.
Icay K, Chen P, Cervera A, Rantanen V, Lehtonen R, Hautaniemi S.
BioData Min. 2016 May 20;9:20. doi: 10.1186/s13040-016-0099-z

MVP/MVP-Fit 2.0 – Macromolecular Visualization and Processing

MVP/MVP-Fit 2.0

:: DESCRIPTION

MVP (Macromolecular Visualization and Processing) is mainly for the illustration and processing of structure-related information which is useful in structure prediction.

MVP-Fit can flexibly move only one domain of the whole model during the fitting process and still keep all the geometric restraints of bond lengths, bond angles and steric clashes for the model.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows
:: DOWNLOAD

 MVP, MVP-Fit

:: MORE INFORMATION

Citation

D Xu, Y Zhang,
MVP-Fit: A Convenient Tool for Flexible Fitting of Protein Domain Structures with Cryo-Electron Microscopy Density Map ,
(2011, in preparation).

BioC 1.1 – A Minimalist Approach to Interoperability for Biomedical Text Processing

BioC 1.1

:: DESCRIPTION

BioC is a simple XML format to share text documents and annotations. It allows a large number of different annotations to be represented. We provide simple code to hold this data, read it and write it back to XML files, and perform some sample processing.

::DEVELOPER

BioC Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java / C++

:: DOWNLOAD

 BioC 

:: MORE INFORMATION

Citation

Database (Oxford). 2013 Sep 18;2013:bat064. doi: 10.1093/database/bat064. Print 2013.
BioC: a minimalist approach to interoperability for biomedical text processing.
Comeau DC, Islamaj Doğan R, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ.

BetaMol v0.92d – Molecular Modeling, Analysis, and Processing software

BetaMol v0.92d

:: DESCRIPTION

BetaMol is a molecular modeling, analysis, and processing software completely based on the theory of the Voronoi diagram, the quasi-triangulation, and the Beta-complex.

::DEVELOPER

Voronoi Diagram Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BetaMol

:: MORE INFORMATION

Citation

Youngsong Cho, Jae-Kwan Kim, Joonghyun Ryu, Chung-In Won, Chong-Min Kim, Donguk Kim, and Deok-Soo Kim,
BetaMol: a molecular modeling, analysis and visualization software based on the beta-complex and the quasi-triangulation,
Journal of Advanced Mechanical Design, Systems, and Manufacturing, Vol.6, Issue 3, pp. 389-403, 2012

RobiNA 1.2.4 – Open Source Microarray and RNA-Seq Processing

RobiNA 1.2.4

:: DESCRIPTION

RobiNA is an integrated solution that consolidates all steps of RNA-Seq-based differential gene-expression analysis in one user-friendly cross-platform application featuring a rich graphical user interface. RobiNA accepts raw FastQ files, SAM/BAM alignment files and counts tables as input. It supports quality checking, flexible filtering and statistical analysis of differential gene expression based on state-of-the art biostatistical methods developed in the R/Bioconductor projects. In-line help and a step-by-step manual guide users through the analysis.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 RobiNA

:: MORE INFORMATION

Citation

Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. (2012)
RobiNA: A user-friendly, integrated software solution for RNA-Seq-based transcriptomics.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7.

JADOPPT – Java based AutoDock Preparing and Processing Tool

JADOPPT

:: DESCRIPTION

JADOPPT is a tool for automatically preparing and processing multiple AutoDock results, thus allowing their simultaneous analysis and comparison.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux /MacOs
  • Java

:: DOWNLOAD

JADOPPT

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 15;33(4):583-585. doi: 10.1093/bioinformatics/btw677.
JADOPPT: java based AutoDock preparing and processing tool.
García-Pérez C, Peláez R, Therón R, Luis López-Pérez J.

NGLess 0.6.1 / NG-meta-profiler 0.9.1 – NGS Processing with Less Work

NGLess 0.6.1 / NG-meta-profiler 0.9.1

:: DESCRIPTION

NGLess is a domain-specific language for NGS (next-generation sequencing data) processing.

NG-meta-profiler is a collection of predefined pipelines for processing shotgun metagenomes.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NGLess , NG-meta-profiler

:: MORE INFORMATION

Citation

Microbiome. 2019 Jun 3;7(1):84. doi: 10.1186/s40168-019-0684-8.
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.
Coelho LP, Alves R, Monteiro P, Huerta-Cepas J, Freitas AT, Bork P

htSeqTools 1.31.0 – Quality Control, Visualization and Processing for High-Throughput Sequencing data

htSeqTools 1.31.0

:: DESCRIPTION

htSeqTools is a Bioconductor package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies.

::DEVELOPER

Evarist Planet, Camille Stephan-Otto, Oscar Reina <oscar.reina at irbbarcelona.org>, Oscar Flores, David Rossell

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • R
  • Bioconductor

:: DOWNLOAD

 htSeqTools

:: MORE INFORMATION

Citation

htSeqTools: high-throughput sequencing quality control, processing and visualization in R.
Planet E, Attolini CS, Reina O, Flores O, Rossell D.
Bioinformatics. 2012 Feb 15;28(4):589-90. doi: 10.1093/bioinformatics/btr700.

ChIA-PET 1.0 – Processing of ChIA-PET sequence data

ChIA-PET 1.0

:: DESCRIPTION

ChIA-PET Tool  is a software package for automatic processing of ChIA-PET (Chromatin Interaction Analysis using Paired-End Tag sequencing )sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser

:: DEVELOPER

the Genome Institute of Singapore

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apach
  • MySQL
  • PHP
  • Java
  • R package
  • C Compiler

:: DOWNLOAD

 ChIA-PET 

:: MORE INFORMATION

Citation

ChIA-PET analysis of transcriptional chromatin interactions.
Zhang J, Poh HM, Peh SQ, Sia YY, Li G, Mulawadi FH, Goh Y, Fullwood MJ, Sung WK, Ruan X, Ruan Y.
Methods. 2012 Nov;58(3):289-99.

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