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http://louisville.edu/

Public research university in Louisville, Kentucky. It is part of the Kentucky state university system.

Proper citation: University of Louisville; Kentucky; USA (RRID:SCR_005749) Copy   

•   Source: SciCrunch Registry

http://www.mellon.org/

The Andrew W. Mellon Foundation currently makes grants in five core program areas: * Higher Education and Scholarship * Scholarly Communications and Information Technology * Art History, Conservation, and Museums * Performing Arts * Conservation and the Environment Within each of its core programs, the Foundation concentrates most of its grantmaking in a few areas. Institutions and programs receiving support are often leaders in fields of Foundation activity, but they may also be promising newcomers, or in a position to demonstrate new ways of overcoming obstacles to achieve program goals. Our grantmaking philosophy is to build, strengthen and sustain institutions and their core capacities, rather than be a source for narrowly defined projects. As such, we develop thoughtful, long-term collaborations with grant recipients and invest sufficient funds for an extended period to accomplish the purpose at hand and achieve meaningful results.

Proper citation: Andrew W. Mellon Foundation (RRID:SCR_005864) Copy   

•   Source: SciCrunch Registry

http://www.auanet.org/content/homepage/homepage.cfm

The American Urological Association (AUA), founded in 1902, is the premier professional association for the advancement of urologic patient care, and works to ensure that its more than 18,000 members are current on the latest research and practices in urology. The AUA also pursues its mission of fostering the highest standards of urologic care by providing a wide range of servicesincluding publications, research, the Annual Meeting, continuing medical education (CME) and the formulation of health policy.

Proper citation: American Urological Association (RRID:SCR_005859) Copy   

•   Source: SciCrunch Registry

http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/html/EDASeq.html

Software for numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EDASeq (RRID:SCR_006751) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/polgui/

An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows)

Proper citation: POLGUI - Matlab Polhemus Interface (RRID:SCR_006752) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mubiomics/

A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms. Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier.

Proper citation: mubiomics (RRID:SCR_006785) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.11/bioc/html/ShortRead.html

Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats.

Proper citation: ShortRead (RRID:SCR_006813) Copy   

•   Source: SciCrunch Registry

http://compbio.bccrc.ca/software/mutationseq/

A software suite using feature-based classifiers for somatic mutation prediction from paired tumour/normal next-generation sequencing data. mutationSeq has the advantages of integrating different features (e.g., base qualities, mapping qualities, strand bias, and tailed distance features), and validated somatic mutations to make predictions. Given paired normal/tumour bam files, mutationSeq will output the probability of each candidate site being somatic.

Proper citation: mutationSeq (RRID:SCR_006815) Copy   

•   Source: SciCrunch Registry

http://www.uni-rostock.de/en/

Public university located in Rostock, Mecklenburg-Vorpommern, Germany. Founded in 1419.

Proper citation: University of Rostock; Mecklenburg-Vorpommern; Germany (RRID:SCR_006816) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/RIPSeeker.html

A statistical software package for identifying protein-associated transcripts from RIP-seq experiments. Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.

Proper citation: RIPSeeker (RRID:SCR_006810) Copy   

•   Source: SciCrunch Registry

http://biobricks.org/

The BioBricks Foundation (BBF) is dedicated to advancing synthetic biology to benefit all people and the planet. To achieve this, we must make engineering biology easier, safer, equitable, and more open. We do this in the following ways: by ensuring that the fundamental building blocks of synthetic biology are freely available for open innovation; by creating community, common values and shared standards; and by promoting biotechnology for all constructive interests. We envision a world in which scientists and engineers work together using BioBric parts freely available standardized biological parts to create safe, ethical solutions to the problems facing humanity. We envision synthetic biology as a force for good in the world. We see a future in which architecture, medicine, environmental remediation, agriculture, and many other fields are using the technology of synthetic biology. Our supporters are many and include corporations, individuals, institutions, foundations, government, corporations, and others. Currently, the BBF''s key programs include: * BIOFAB * BioBrick Public Agreement * Technical Standards Framework * Conferences and Workshops * BBF Global Network * OpenWetWare

Proper citation: BioBricks Foundation (RRID:SCR_006779) Copy   

•   Source: SciCrunch Registry

https://www.peprotech.com/

An Antibody supplier

Proper citation: PeproTech (RRID:SCR_006802) Copy   

•   Source: SciCrunch Registry

http://www.lsdfa.org/

Funds innovative research and development in Washington state to promote life sciences competitiveness, enhance economic vitality, and improve health and health care. Its grantmaking opportunities are designed to leverage the state''s investment in research and development by achieving three goals: promoting health; making the life sciences sector more competitive; and strengthening Washington''s economy. LSDF currently offers two different types of granting mechanisms for both for-profit and non-profit organizations in Washington: * Proof of Concept grants to enhance the commercial viability of intellectual property developed by non-profit organizations or enhance the competitiveness of early-stage companies for private equity investment. (This grant mechanism combines the Commercialization and PreCede mechanisms offered in prior years.) * Opportunity grants to fund extraordinary research and development proposals having the ability to significantly leverage LSDF dollars against those from other sources.

Proper citation: Life Sciences Discovery Fund (RRID:SCR_006845) Copy   

•   Source: SciCrunch Registry

http://neuronvisio.org/

A Graphical User Interface for NEURON simulator environment with 3D capabilities. Neuronvisio makes easy to select and investigate sections'''' properties and it offers easy integration with matplotlib for plotting the results. The geometry can be saved using NeuroML and the computational results in a customized and extensible HDF5 format; the results can then be reload in the software and analyzed in a later stage, without re-running the simulation. Featuring 3D visualization of the model with the possibility to change it runtime; creation of vectors to record any variables present in the section; pylab integration to plot directly the result of the simulation; exploration of the timecourse of any variable among time using a color coded scale; saving the results simulation for later analysis; automatic download and running of models in ModelDB.

Proper citation: NeuronVisio (RRID:SCR_006839) Copy   

•   Source: SciCrunch Registry

https://github.com/friend1ws/EBCall

A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies.

Proper citation: EBCall (RRID:SCR_006791) Copy   

•   Source: SciCrunch Registry

http://www.pelfreez-bio.com/

An Antibody supplier

Proper citation: Pel-Freez Biologicals (RRID:SCR_006827) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bamstats/

A GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API.

Proper citation: BAMStats (RRID:SCR_006973) Copy   

•   Source: SciCrunch Registry

http://www.uwyo.edu/

Public land grant research university in Laramie, Wyoming.

Proper citation: University of Wyoming; Wyoming; USA (RRID:SCR_007020) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.9/bioc/html/RamiGO.html

Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.

Proper citation: RamiGO (RRID:SCR_006922) Copy   

•   Source: SciCrunch Registry

http://www.seqan.de/projects/razers/

A read mapping software program with adjustable sensitivity based on counting q-grams. RazerS 3 supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers? bit-vector algorithm for verification, memory saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular long reads with many errors.

Proper citation: RazerS (RRID:SCR_006889) Copy   

•   Source: SciCrunch Registry