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http://core-genomics.blogspot.de/
This blog focusses on next-generation sequencing and microarray technologies.
Proper citation: CoreGenomics (RRID:SCR_011985) Copy
A leading source of news on technology and innovation in life sciences IT, informatics, genomics, next-gen, drug discovery, development, and clinical trials.
Proper citation: Bio-IT World (RRID:SCR_011986) Copy
http://www.mutationtaster.org/
Evaluates disease-causing potential of sequence alterations.
Proper citation: MutationTaster (RRID:SCR_010777) Copy
http://hyperbrowser.uio.no/hb/
A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets.
Proper citation: Genomic HyperBrowser (RRID:SCR_010909) Copy
https://genome-cancer.ucsc.edu/
A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets.
Proper citation: UCSC Cancer Genomics Browser (RRID:SCR_011796) Copy
http://weizhong-lab.ucsd.edu/metagenomic-analysis/
A customizable web server for fast metagenomic analysis.
Proper citation: WebMGA (RRID:SCR_011951) Copy
Blog including established profound know-how and proprietary protocols to cover a broad range of applications.
Proper citation: NGS Expert Blog (RRID:SCR_013218) Copy
A sequence verification pipeline where users can submit trace files to verify if a clone''s physical sequence matches its reference sequence.
Proper citation: GenoREAD (RRID:SCR_012007) Copy
http://cdwscience.blogspot.fr/
A blog about genetics, genomics, and medical research.
Proper citation: My Biomedical Informatics Blog (RRID:SCR_012011) Copy
http://zope.bioinfo.cnio.es/plan2l/plan2l.html
A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned.
Proper citation: PLAN2L (RRID:SCR_013346) Copy
A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis.
Proper citation: CRAVAT (RRID:SCR_012776) Copy
https://github.com/common-workflow-language/cwltool
Reference implementation of the Common Workflow Language standards. It provides complete features and tools and comprehensive validation of CWL. The reference implementation consists of two packages. The cwltool package is the primary Python module containing the reference implementation in the cwltool module and console executable by the same name. The cwlref-runner package is optional and provides an additional entry point under the alias cwl-runner, which is the implementation-agnostic name for the default CWL interpreter installed on a host.
Proper citation: cwltool (RRID:SCR_015528) Copy
A web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: DSAP (RRID:SCR_013352) Copy
http://collaborations.gis.a-star.edu.sg/~cmb6/TherMos/
Software used for estimating protein-DNA binding energies from in vivo binding profiles. It is a de novo motif discovery algorithm that exploits the information in transcription factor ChIP-seq or ChIP-exo datasets based on a more natural thermodynamic formalism., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TherMos (RRID:SCR_002790) Copy
http://cran.r-project.org/web/packages/enviPick/
Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot.
Proper citation: enviPick (RRID:SCR_003059) Copy
https://www.apbenson.com/cyrillic-downloads
Software application for pedigree drawing with fully integrated risk analysis and support for industry standard databases (MS Access and Corel Paradox). It is designed for genetic counselors and others who work with patients. Cyrillic 2 draws pedigrees, works with genetic marker data, lets you do haplotyping and allows exports to a range of linkage analysis packages.
Proper citation: CYRILLIC (RRID:SCR_001823) Copy
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. It works along with the Open Bioinformatics Foundation, who generously host it''s website, bug tracker, and mailing lists. Sponsor: This resource is supported by the Open Bioinformatics Foundation. Keywords: Tool, Software, Python, Biological, Computation, Bioinformatics,
Proper citation: Biopython (RRID:SCR_007173) Copy
http://www.well.ox.ac.uk/platypus
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool designed for efficient and accurate variant detection in high throughput sequencing data. Haplotype based variant caller for next generation sequence data.
Proper citation: Platypus (RRID:SCR_005389) Copy
http://huttenhower.sph.harvard.edu/galaxy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: LEfSe (RRID:SCR_014609) Copy
https://ccg.murdoch.edu.au/yabi/login/?next=/yabi/
A web-based analytical environment framework for bioinformatics applications that can be customized for a diverse range of -omics applications. The software system is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC environments at its core, it then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. It can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts.
Proper citation: Yabi (RRID:SCR_005359) Copy
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