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http://depts.washington.edu/biowww/

A department within the University of Washington which focuses on both undergraduate and postgraduate education in biochemistry.

Proper citation: UW Department of Biochemistry (RRID:SCR_000149) Copy   

•   Source: SciCrunch Registry
  

http://www.scienceexchange.com/facilities/edgebio

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A contract research organization that provides genomics services such as sequencing, bioinformatics, NGS data analysis and whole exome sequencing. EdgeBio is a CLIA-approved service provider.

Proper citation: EdgeBio (RRID:SCR_000183) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/MIMOSA.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.

Proper citation: MIMOSA (RRID:SCR_000184) Copy   

•   Source: SciCrunch Registry
  

http://www.genetex.com/

An antibody supplier for the purposes of life science and biomedical research. This company has a wide variety of immunological reagents that focus on areas of research such as cancer, cell biology, epigenetics, immunology and infectious diseases.

Proper citation: GeneTex (RRID:SCR_000069) Copy   

•   Source: SciCrunch Registry
  

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

Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).

Proper citation: nFuse (RRID:SCR_000066) Copy   

•   Source: SciCrunch Registry
  

https://www.schrodinger.com/glide

Software package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Used in drug development for predicting protein ligand binding modes and ranking ligands via high throughput virtual screening.

Proper citation: Glide (RRID:SCR_000187) Copy   

•   Source: SciCrunch Registry
  

http://www.ccdc.cam.ac.uk/Solutions/GoldSuite/Pages/GOLD.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software for virtual screening and identifying the binding mode of active molecules. It is comprehensively validated, widely used, and allows for high database enrichments. The software utilizes a novel methodology which avoids computationally expensive sequential docking of ligands into multiple protein structures.

Proper citation: GOLD (RRID:SCR_000188) Copy   

•   Source: SciCrunch Registry
  

http://www.unavco.org/data/web-services/documentation/unavco-ws-api/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Web services to access UNAVCO data collection. Adding /gps, /met, /pore, /tilt, and /strain gives the sensor JSON description.

Proper citation: UNAVCO Geodetic Web Services (RRID:SCR_000181) Copy   

•   Source: SciCrunch Registry
  

http://code.google.com/p/gasv/

Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions.

Proper citation: GASV (RRID:SCR_000061) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/chipmeta/

Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets.

Proper citation: ChIPmeta (RRID:SCR_000054) Copy   

•   Source: SciCrunch Registry
  

http://discover.nci.nih.gov/gominer/GoCommandWebInterface.jsp

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A web program that organizes lists of genes of interest (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology and automates the analysis of multiple microarrays then integrates the results across all of them in exportable output files and visualizations. High-Throughput GoMiner is an enhancement of GoMiner and is implemented with both a command line interface and a web interface. The program can also: efficiently perform automated batch processing of an arbitrary number of microarrays; produce a human- or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories; integrate the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories; provide a fast form of false discovery rate multiple comparisons calculation; and provide annotations and visualizations for relating transcription factor binding sites to genes and GO categories.

Proper citation: High-Throughput GoMiner (RRID:SCR_000173) Copy   

•   Source: SciCrunch Registry
  

https://github.com/SciLifeLab/facs

Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.

Proper citation: FACS (RRID:SCR_000055) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/batman-seq/

A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment.

Proper citation: Batman-Seq (RRID:SCR_000048) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/bait/

Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

Proper citation: BAIT (RRID:SCR_000511) Copy   

•   Source: SciCrunch Registry
  

http://www.arb-home.de/

Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations.

Proper citation: ARB project (RRID:SCR_000515) Copy   

•   Source: SciCrunch Registry
  

http://www.ecnp.eu/

A pan-European scientific association to encourage research across the neurosciences and to translate new knowledge on fundamental disease mechanisms into new medicines and clinical applications. As an interdisciplinary forum for the science and treatment of disorders of the brain, they promote the communication and cross- fertilization of high-quality experimental and clinical research across the field of neuroscience. ECNP is a non-profit member-based association, independently governed and self-funded. ECNP is a public-interest-serving entity.

Proper citation: ECNP (RRID:SCR_000501) Copy   

•   Source: SciCrunch Registry
  

http://www.fluwikie.com/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Flu Wikie is a topical portal on the flu. Major categories include health, Flu Symptoms, Avian Influenza, Swine Flu, Cold, Vaccination, Pandemic, Vitamin D, and Immune System. Many articles on topic are included.

Proper citation: FluWikie.com (RRID:SCR_000506) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/iASeq.html

Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.

Proper citation: iASeq (RRID:SCR_000420) Copy   

•   Source: SciCrunch Registry
  

https://github.com/yhwu/matchclips/

Software program that detects the precise break points of Copy number variations (CNVs) through a fuzzy string matching algorithm using both CIGAR and POS information. In case the two break points of a CNV are in repeated regions and the break points are not unique, it reports the range where the break points can slide.

Proper citation: MATCHCLIP (RRID:SCR_000541) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/mri_lbptop/

The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology.

Proper citation: Local Binary Pattern Analysis Tools for MR Brain Images (RRID:SCR_000412) Copy   

•   Source: SciCrunch Registry