Tag: Context

Peakhood v0.3 – Individual Site Context Extraction for CLIP-Seq Peak Regions

Peakhood v0.3

:: DESCRIPTION

Peakhood is a tool that takes a set of CLIP-seq peak regions, and for each region individually extracts the most likely site context (transcript or genomic).

::DEVELOPER

Bioinformatics Group Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Conda

:: DOWNLOAD

Peakhood

:: MORE INFORMATION

Citation

Uhl M, Rabsch D, Eggenhofer F, Backofen R.
Peakhood: individual site context extraction for CLIP-seq peak regions.
Bioinformatics. 2021 Nov 4:btab755. doi: 10.1093/bioinformatics/btab755. Epub ahead of print. PMID: 34734974.

Systrip 1.0 – Investigation of Time-series data in the context of Metabolic Networks

Systrip 1.0

:: DESCRIPTION

Systrip is a visual environment for the analysis of time-series data in the context of biological networks. Systrip gathers bioinformatics and graph theoretical algorithms that can be assembled in different ways to help biologists in their visual mining process.

::DEVELOPER

Romain Bourqui

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Systrip

:: MORE INFORMATION

ContextMap 2.7.9 – Context-based mapping of RNA-seq data

ContextMap 2.7.9

:: DESCRIPTION

ContextMap is a very accurate read mapping tool for data from RNA-seq experiments. It can be used to refine mappings provided by other tools or as a standalone program.

::DEVELOPER

Institute for Bioinformatics, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 ContextMap

:: MORE INFORMATION

Citation

ContextMap 2: fast and accurate context-based RNA-seq mapping.
Bonfert T, Kirner E, Csaba G, Zimmer R, Friedel CC.
BMC Bioinformatics. 2015 Apr 17;16(1):122. doi: 10.1186/s12859-015-0557-5.

Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel.
A context-based approach to identify the most likely mapping for RNA-seq experiments.
BMC Bioinformatics, vol 13(Suppl 6), pp. S9, 2012.

PinSnps – Structural and Functional analysis of SNPs in the Context of Protein Interaction Networks

PinSnps

:: DESCRIPTION

PinSnps is an interactive tool for the analysis of common variants, disease-related single-nucleotide polymorphisms (SNPs), Post-Translational Modifications (PTMs) and related functional sites mapped onto human protein interaction networks. One can search for and retrieve information about SNPs data and interacting proteins of the query.

::DEVELOPER

Fraternali lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Lu HC, Herrera Braga J, Fraternali F.
PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks.
Bioinformatics. 2016 Aug 15;32(16):2534-6. doi: 10.1093/bioinformatics/btw153. Epub 2016 Mar 24. PMID: 27153707; PMCID: PMC4978923.

CASPER 0.8.2 – Context-Aware Scheme for Paired-End Read

CASPER 0.8.2

:: DESCRIPTION

CASPER is a state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads.

::DEVELOPER

Data Science Laboratory, Seoul National University.

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CASPER

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014;15 Suppl 9:S10. doi: 10.1186/1471-2105-15-S9-S10. Epub 2014 Sep 10.
CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing.
Kwon S, Lee B, Yoon S.

GSCA 2.0 – Gene Set Context Analysis

GSCA 2.0

:: DESCRIPTION

GSCA is an open source software package to transform massive amounts of Publicly available gene Expression Data (PED) into a tool for making new discoveries.

::DEVELOPER

Zhicheng Ji

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 GSCA

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2016 Jan 8;44(1):e8. doi: 10.1093/nar/gkv873. Epub 2015 Sep 8.
Turning publicly available gene expression data into discoveries using gene set context analysis.
Ji Z, Vokes SA, Dang CV, Ji H

PathRNet – Robust Inference of the Context Specific Structure and Temporal Dynamics of Gene Regulatory Network

PathRNet

:: DESCRIPTION

A novel network model PathRNet and a reconstruction approach PATTERN are proposed for reconstructing the context specific time varying regulatory networks by integrating microarray gene expression profiles and existing knowledge of pathways and transcription factors.

::DEVELOPER

PathRNet Team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • MatLab

:: DOWNLOAD

 PathRNet

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Dec 1;11 Suppl 3:S11. doi: 10.1186/1471-2164-11-S3-S11.
Robust inference of the context specific structure and temporal dynamics of gene regulatory network.
Meng J1, Lu M, Chen Y, Gao SJ, Huang Y.

PageMan 0.12 – Annotates, Investigates, and Condenses Microarray data in the Context of Functional Ontologies

PageMan 0.12

:: DESCRIPTION

PageMan is a tool to get a quick overview of multiparallel experiments. PageMan also helps comparing experiments from different organisms.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 PageMan

:: MORE INFORMATION

Citation

Usadel B, Nagel A, Steinhauser D, Gibon Y, Blaesing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR, Stitt M (2006)
PageMan an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments,
BMC Bioinformatics 18:7:535

DPUC 2.08 – Using Context to Improve Protein Domain Identification

DPUC 2.08

:: DESCRIPTION

DPUC (Domain Prediction Using Context) extends your Pfam predictions without loss of precision using domain context!

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DPUC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Mar 31;12:90. doi: 10.1186/1471-2105-12-90.
Using context to improve protein domain identification.
Ochoa A1, Llinás M, Singh M.

BaobabLuna 1.1 beta – Manipulation of Signed Permutations in the Context of Genomic Evolution

BaobabLuna 1.1 beta

:: DESCRIPTION

BaobabLUNA is a java framework to deal with permutations that represent genomes in rearrangement analysis. baobabLUNA contains a collection of classes for building breakpoint graphs (the basic structures behind the work on genome rearrangements), performing reversals, calculating reversal distances, sorting permutations. Includes a text representation for the breakpoint graph.baobabLUNA is only able to deal with unichromosomal genomes and its main functionality is the implementation of an algorithm that gives a compact representation of the space of all solutions of the sorting by reversals problem, that is, a representation of all optimal sequences of reversals that sort one genome into another.

::DEVELOPER

Marília D. V. Braga

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 BaobabLuna

:: MORE INFORMATION

Citation

Braga M. D. V.,
baobabLUNA: the solution space of sorting by reversals,
Bioinformatics, vol. 25, no. 14, 1833–1835, 2009.