OncoRep – Oncogenomics Report

OncoRep

:: DESCRIPTION

OncoRep is a fully automated RNA-Seq based report for patients with (breast) cancer, which includes molecular classification, detection of altered genes, detection of altered pathways, identification of gene fusion events, identification of clinical actionable mutations (in coding regions) and identification of treatable target structures.

::DEVELOPER

The Su Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows
  • R

:: DOWNLOAD

 OncoRep

:: MORE INFORMATION

Citation:

OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing.
Meißner T, Fisch KM, Gioia L, Su AI.
BMC Med Genomics. 2015 May 21;8:24. doi: 10.1186/s12920-015-0095-z.

MultiQC 0.6 – Aggregate Results from Bioinformatics Analyses across many samples into a single Report

MultiQC 0.6

:: DESCRIPTION

MultiQC is a modular tool to aggregate results from bioinformatics analyses across many samples into a single report.. It’s a general use tool, perfect for summarising the output from numerous bioinformatics tools.

::DEVELOPER

Phil Ewels

:: SCREENSHOTS

MultiQC

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 MultiQC

:: MORE INFORMATION

Citation

MultiQC: Summarize analysis results for multiple tools and samples in a single report.
Ewels P, Magnusson M, Lundin S, Käller M.
Bioinformatics. 2016 Jun 16. pii: btw354.

Nozzle 1.1-1 – Generation of Reports in High-throughput data analysis pipelines

Nozzle 1.1-1

:: DESCRIPTION

Nozzle is an R package for generation of reports in high-throughput data analysis pipelines.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

  Nozzle

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Apr 15;29(8):1089-91. doi: 10.1093/bioinformatics/btt085. Epub 2013 Feb 17.
Nozzle: a report generation toolkit for data analysis pipelines.
Gehlenborg N1, Noble MS, Getz G, Chin L, Park PJ.

ReportingTools 2.8.0 – Tools for Making Microarray and Sequencing Data Reports in various Formats

ReportingTools 2.8.0

:: DESCRIPTION

The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel.

:: DEVELOPER

Jason A. Hackney <hackney.jason at gene.com>, Melanie Huntley, Jessica L. Larson, Christina Chaivorapol, Gabriel Becker <gmbecker at ucdavis.edu>, and Josh Kaminker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

  ReportingTools

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 18.
ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.
Huntley MA, Larson JL, Chaivorapol C, Becker G, Lawrence M, Hackney JA, Kaminker JS.

bamchop – Generate Targeted Resequencing Report from BAM File

bamchop

:: DESCRIPTION

bamchop is a robust program to efficiently summarize key statistical metrics of HTS data stored in BAM files, and to visually present the results in a formatted report.

::DEVELOPER

The Department of Biomedical and Health Informatics (DBHi)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • R
  • LaTeX

:: DOWNLOAD

 bamchop

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2013;14 Suppl 11:S3. doi: 10.1186/1471-2105-14-S11-S3. Epub 2013 Sep 13.
Efficient digest of high-throughput sequencing data in a reproducible report.
Zhang Z, Leipzig J, Sasson A, Yu AM, Perin JC, Xie HM, Sarmady M, Warren PV, White PS.

SBML2LATEX 0.9.9 – Conversion of SBML files into Human-readable Reports

SBML2LATEX 0.9.9

:: DESCRIPTION

SBML2LATEX is a tool to convert files in the System Biology Markup Language SBML) format into LATEX files.

SBML2LATEX Online Version

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

SBML2LATEX

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

  SBML2LATEX

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jun 1;25(11):1455-6. doi: 10.1093/bioinformatics/btp170. Epub 2009 Mar 23.
SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.
Dräger A, Planatscher H, Motsou Wouamba D, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A.

BioParser 1.2.3 – Parsing Sequence Similarity Analysis Reports

BioParser 1.2.3

:: DESCRIPTION

BioParser is a Perl program for parsing sequence similarity analysis reports.

::DEVELOPER

Department of Biochemistry and Molecular Biology, Oswaldo Cruz Institute, Brazil.

:: SCREENSHOTS

BioParser

:: REQUIREMENTS

  • Linux / Windows
  • Perl
  • BioPerl
  • MySQL

:: DOWNLOAD

 BioParser

:: MORE INFORMATION

Citation

Appl Bioinformatics. 2006;5(1):49-53.
BioParser: a tool for processing of sequence similarity analysis reports.
Catanho M, Mascarenhas D, Degrave W, de Miranda AB.