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.

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

Hautaniemi Lab

:: 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

BioMAJ 3.0.13 – Workflow Engine Dedicated to Data Synchronization and Processing

BioMAJ 3.0.13

:: DESCRIPTION

BioMAJ (BIOlogie Mise A Jour) is a workflow engine dedicated to data synchronization and processing. The Software automates the update cycle and the supervision of the locally mirrored databank repository.

::DEVELOPER

BioMAJ TEam

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac / Linux
  • Java
  • ant >= 1.7.0.

:: DOWNLOAD

 BioMAJ

:: MORE INFORMATION

Citation

Olivier Filangi at el. 2008
BioMAJ: A flexible framework for databanks synchronization and processing
Bioinformatics 2008 24(16):1823-1825;

RPASuite v0.02 – RNA Processing Analysis Suite

RPASuite v0.02

:: DESCRIPTION

RPASuite is a computational pipeline to identify differentially and coherently processed transcripts using RNA-seq data obtained from multiple tissue or cell lines.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RPASuite

:: MORE INFORMATION

Citation

Pundhir S and Gorodkin J. (2015)
Differential and coherent processing patterns from small RNAs.
Sci Rep. 5:12062

ArrayExpressHTS 1.18.0 – RNA-seq data Processing and Quality Assessment

ArrayExpressHTS 1.18.0

:: DESCRIPTION

ArrayExpressHTS is an R and Bioconductor RNA-seq processing pipeline that highly utilizes distributed computing for data processing and quality assessment of High-Throughput Sequencing experiments and datasets

::DEVELOPER

EBI.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

  ArrayExpressHTS

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Mar 15;27(6):867-9. doi: 10.1093/bioinformatics/btr012. Epub 2011 Jan 13.
A pipeline for RNA-seq data processing and quality assessment.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.

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

IntegrationMap / IntegrationSeq – Integration Site Mapping and Profiling / Sequence Trimming and Processing Tool

IntegrationMap / IntegrationSeq

:: DESCRIPTION

IntegrationMap can be used to determine and profile integration sites of viruses or viral vectors on a chromosomal and genomic level.

IntegrationSeq can be used to prepare raw files from an genetic analyzer for mapping to the human genome.

::DEVELOPER

HUSAR Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Methods Inf Med. 2007;46(5):542-7.
New bioinformatic strategies to rapidly characterize retroviral integration sites of gene therapy vectors.
Giordano FA1, Hotz-Wagenblatt A, Lauterborn D, Appelt JU, Fellenberg K, Nagy KZ, Zeller WJ, Suhai S, Fruehauf S, Laufs S.

snapCGH 1.38.0 – Segmentation, Normalisation And Processing of Array CGH data

snapCGH 1.38.0

:: DESCRIPTION

snapCGH is a softwaer for the analysis of array CGH data. It has been written to be compatible with limma so that the user can apply all of the preprocessing functions available within limma to array CGH data.

::DEVELOPER

Computational Biology Group, Department of Oncology, University of Cambridge

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 snapCGH

:: MORE INFORMATION