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.

ASAP 1.1.7 – Automated Sequence data Processing on Computer Clusters

ASAP 1.1.7

:: DESCRIPTION

ASAP (Advanced Sequence Automated Pipeline)is an open source pipeline designed to assist users in managing various jobs associated with processing HiSeq data on a cluster or in serial. . The software was designed to alleviate these issues by providing a modular system to allow users with different needs to process their data with a minimal amount of effort. In addition to minimizing human involvement, ASAP is designed to work on the researcher’s local computer cluster, if one is available

::DEVELOPER

Chun Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ASAP

:: MORE INFORMATION

Citation

BMC Res Notes. 2013 Jan 4;6:5. doi: 10.1186/1756-0500-6-5.
ASAP: an environment for automated preprocessing of sequencing data.
Torstenson ES1, Li B, Li C.

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