Tools   Select Another Resource Report Type

http://fx.gmi.ac.kr/

A user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing.

Proper citation: FX (RRID:SCR_011902) Copy   

•   Source: SciCrunch Registry

http://www.eecs.ucf.edu/~xiaoman/SIOMICS/SIOMICS.html

A software to de novo identify motifs in large sequence datasets such as those from ChIP-seq experiments.

Proper citation: SIOMICS (RRID:SCR_011990) Copy   

•   Source: SciCrunch Registry

http://www.litinspector.org/

A literature search tool providing gene and signal transduction pathway mining within NCBI''''s PubMed database. Its sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets you analyze signal transduction pathways, diseases and tissue associations in a snap. Note: LitInspector has become part of the Literature & Pathways module of the Genomatix Software Suite.

Proper citation: LitInspector (RRID:SCR_011870) Copy   

•   Source: SciCrunch Registry

http://derisilab.ucsf.edu/data/microarray/index.html

A public source for microarray protocols and software.

Proper citation: Microarrays.org (RRID:SCR_011992) Copy   

•   Source: SciCrunch Registry

http://vina.scripps.edu/

An open-source program for doing molecular docking.

Proper citation: AutoDock Vina (RRID:SCR_011958) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/vegan/index.html

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Proper citation: vegan (RRID:SCR_011950) Copy   

•   Source: SciCrunch Registry

http://www.exelixis-lab.org/software.html

A tool for delimiting species on phylogenies and evolutionary placements.

Proper citation: PTP (RRID:SCR_011952) Copy   

•   Source: SciCrunch Registry

http://www.cs.helsinki.fi/u/lmsalmel/coral/

An error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer.

Proper citation: Coral (RRID:SCR_011849) Copy   

•   Source: SciCrunch Registry

http://opm.phar.umich.edu/

Database that provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal.

Proper citation: Orientations of Proteins in Membranes database (RRID:SCR_011961) Copy   

•   Source: SciCrunch Registry

http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software/cobalten

A comprehensive database that gathers all prediction outputs concerning complete prokaryotic proteomes. It is a client-server application, with the server installed and staying at Biogenouest bioinformatics platform, keeping all needed pre-computed genomic data, while the CoBaltDB Client or GUI is a Java application which communicates with the server via web-services. The CoBaltDB Client needs to be downloaded on your computer.

Proper citation: CoBaltDB (RRID:SCR_011970) Copy   

•   Source: SciCrunch Registry

http://scalpel.sourceforge.net/

A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).

Proper citation: Scalpel (RRID:SCR_012107) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/denovogui/

Software providing a user-friendly and lightweight graphical user interface for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics.

Proper citation: DeNovoGUI (RRID:SCR_012074) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/krux/

An algorithm implemented in Matlab, Python and R that uses matrix multiplications to simultaneously calculate the Kruskal-Wallis test statistic for several millions of marker-trait combinations at once.

Proper citation: kruX (RRID:SCR_012076) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/snpratiotest/

Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway.

Proper citation: SNP ratio test (RRID:SCR_012070) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/compomics-utilities/

A software library containing code shared by many research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc. This library can be of use to other research groups doing computational proteomics.

Proper citation: compomics-utilities (RRID:SCR_012073) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/campways/

Software that provides one-to-many alignments of reactions in a pair of metabolic pathways.

Proper citation: CAMPways (RRID:SCR_012072) Copy   

•   Source: SciCrunch Registry

http://toxtree.sourceforge.net/

A full-featured and flexible user-friendly open source software application, which is able to estimate toxic hazard by applying a decision tree approach.

Proper citation: Toxtree (RRID:SCR_012086) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/viewmol/

Software providing a graphical front end for computational chemistry programs.

Proper citation: Viewmol (RRID:SCR_012088) Copy   

•   Source: SciCrunch Registry

http://toxmatch.sourceforge.net/

A software tool to facilitate chemical similarity calculations.

Proper citation: Toxmatch (RRID:SCR_012087) Copy   

•   Source: SciCrunch Registry

http://qutemol.sourceforge.net/

Open source (GPL) software providing an interactive, high quality molecular visualization system.

Proper citation: QuteMol (RRID:SCR_012089) Copy   

•   Source: SciCrunch Registry