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http://jilab.biostat.jhsph.edu/software/tilemap/index.htm

Software tool for microarray tile mapping. It utilizes ChIP-chip peak calling to identify genomic loci that show transcriptional activities and transcription factor binding patterns of interest.

Proper citation: TileMap (RRID:SCR_001589) Copy   

•   Source: SciCrunch Registry

http://sherlock.ucsf.edu/

Service to discover disease genes in GWAS using eQTL signature matching by simply submitting your list of GWAS associations (SNPs and p-values). It is important to upload all SNPs in your association study, not just the top hits. Sherlock may be able to group multiple lower-confidence SNPs to discover functionally-important genes.

Proper citation: Sherlock (RRID:SCR_001628) Copy   

•   Source: SciCrunch Registry

http://bios.unc.edu/~weisun/software/asSeq.htm

Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq

Proper citation: asSeq (RRID:SCR_001625) Copy   

•   Source: SciCrunch Registry

https://github.com/beiko-lab/gengis

A bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. It provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.

Proper citation: GenGIS (RRID:SCR_001465) Copy   

•   Source: SciCrunch Registry

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

A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing enrichment. It does not rely on a specific array technology (although the array should be a tiling array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.

Proper citation: ACME (RRID:SCR_001464) Copy   

•   Source: SciCrunch Registry

http://eddylab.org/software.html

Software library containing tools for statistical manipulations of data. Tools include profile hidden Markov models for biological sequence analysis, RNA structure analysis, and a prototype noncoding RNA genefinder.

Proper citation: Eddy Lab Software (RRID:SCR_001458) Copy   

•   Source: SciCrunch Registry

http://alpha-1foundation.org/

A not-for-profit organization to increase awareness of and find a cure for Alpha-1 Antitrypsin Deficiency that has invested nearly $39 million to support Alpha-1 research at more than 70 institutions in North America, Europe and Australia. They are dedicated to providing the leadership and resources that will result in increased research, improved health, worldwide detection, and a cure for Alpha-1 Antitrypsin Deficiency. The Foundation has developed a solid infrastructure to promote research and the development of new therapies for improving the quality of life for those diagnosed with Alpha-1. It has fostered collaborations with investigators throughout the United States and Europe, working closely with the National Institutes of Health (NIH), the Food and Drug Administration (FDA), individuals affected by Alpha-1, and the pharmaceutical industry to expedite the development of improved therapies. The Foundation participates in industry and government liaison groups and develops strategic alliances with government, industry and other national and international health and research organizations. They're the source for all Alpha-1 and COPD-related info.

Proper citation: Alpha-1 Foundation (RRID:SCR_001498) Copy   

•   Source: SciCrunch Registry

http://www.healthystudy.org/

Primary prevention trial conducted in 42 middle schools at 7 locations across the US to impact risk factors for type 2 diabetes in adolescents. Students were recruited at the start of 6th grade (fall 2006) and followed to the end of 8th grade (spring 2009). Half of the schools were randomized to receive an intervention that integrated four components: the school nutrition environment, physical education class activities, behavior change initiatives, and educational and promotional communications activities.

Proper citation: HEALTHY study (RRID:SCR_001530) Copy   

•   Source: SciCrunch Registry

http://www.immuneprofiling.org/

Consortium established to capitalize on recent advances in immune profiling methods in order to create a novel public resource that characterizes diverse states of the human immune system following infection; prior to and following vaccination against an infectious disease; or prior to and following treatment with an immune adjuvant that targets a known innate immune receptor(s). Through this program, well-characterized human cohorts are studied using a variety of modern analytic tools, including multiplex transcriptional, cytokine, and proteomic assays; multiparameter phenotyping of leukocyte subsets; assessment of leukocyte functional status; and multiple computational methods. Centralized research resources and a comprehensive, centralized database will be constructed for use by the greater scientific community. The information gained from the program will provide a comprehensive understanding of the human immune system and its regulation, and will reveal novel associations between components of the immune system and other biological systems, identify novel immune mediators and pathways, establish predictors of vaccine safety in different populations, and enable the rapid evaluation of different vaccine formulations and administration regimens in human populations.

Proper citation: Human Immunology Project Consortium (RRID:SCR_001491) Copy   

•   Source: SciCrunch Registry

http://drcrnet.jaeb.org/

A collaborative network to facilitate multicenter clinical research of diabetic retinopathy, diabetic macular edema and associated conditions. It supports the identification, design, and implementation of multicenter clinical research initiatives focused on diabetes-induced retinal disorders. Principal emphasis is placed on clinical trials, but epidemiologic outcomes and other research may be supported as well. It currently includes over 109 participating sites (offices) with over 320 physicians throughout the United States. Closed and active studies are listed along with the associated protocols, public datasets, and publications.

Proper citation: Diabetic Retinopathy Clinical Research Network (RRID:SCR_001514) Copy   

•   Source: SciCrunch Registry

https://github.com/uci-cbcl/PyLOH

Software for deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. The model resolves the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity - within an unified probabilistic framework.

Proper citation: PyLOH (RRID:SCR_001511) Copy   

•   Source: SciCrunch Registry

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

Software that infers biological processes which are active in individual gene sets from corresponding microarray measurements. It achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets.

Proper citation: CoGAPS (RRID:SCR_001479) Copy   

•   Source: SciCrunch Registry

http://direcnet.jaeb.org/

Network of clinical centers and a coordinating center that investigate the potential use of glucose monitoring technology and its impact on the management of type 1 diabetes in children. Specific goals for the network include the following: * Assess the accuracy of continuous monitoring devices in order to determine if these devices are useful in improving glycemic control and preventing hypoglycemia in children with T1DM. * Determine the optimal utilization of continuous glucose monitors in the management of T1DM in children. * Assess the impact of continuous glucose monitoring on quality of life for the child and family. * Develop tools for the child and parents to use for incorporating continuous glucose monitors into diabetes self-management. * To assess possible changes in neurocognitive function and how it relates to frequency of hypoglycemia in young children with type 1 diabetes. * Evaluate and develop distinct, age-appropriate treatment approaches to T1DM in children. * Use continuous glucose monitoring to characterize the glycemic profile of nondiabetic children. * Develop statistical methods for the analysis of continuous glucose monitoring data. Closed and active studies are listed along with the associated protocols, public datasets, and publications.

Proper citation: Diabetes Research in Children Network (RRID:SCR_001512) Copy   

•   Source: SciCrunch Registry

http://nebula.curie.fr/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Web portal that allows users to analyze ChIP-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Nebula (RRID:SCR_001516) Copy   

•   Source: SciCrunch Registry

https://github.com/ElementoLab/ChIPseeqer

Software that provides a comprehensive framework for the analysis of ChIP-seq data.

Proper citation: ChIPseeqer (RRID:SCR_001545) Copy   

•   Source: SciCrunch Registry

https://www.searchfordiabetes.org/

National multi-center study aimed at understanding more about diabetes among children and young adults in the United States less than 20 years of age in six geographically dispersed populations that encompass the ethnic diversity of the United States. SEARCH has been helping to find answers about the types of diabetes, its complications, and how having diabetes affects the lives of children and young adults. There are more than 20,000 study participants representing all different racial and ethnic backgrounds who have helped SEARCH determine the extent of diabetes in the community and its impact on different populations. The SEARCH Study invites Investigators interested in childhood Diabetes Research to collaborate on matters of interest to the field of childhood Diabetes.

Proper citation: SEARCH for Diabetes in Youth (RRID:SCR_001540) Copy   

•   Source: SciCrunch Registry

http://www.niddklabs.org

Consortium comprised of six clinical centers and a data coordinating center to facilitate coordinated clinical, epidemiological, and behavioral research in the field of bariatric surgery, through the cooperative development of common clinical protocols and a bariatric surgery database that will collect information from participating clinical centers. LABS will help pool the necessary clinical expertise and administrative resources to facilitate the conduct of multiple clinical studies in a timely, efficient manner. Also, the use of standardized definitions, clinical protocols, and data-collection instruments will enhance the investigator's ability to provide meaningful evidence-based recommendations for patient evaluation, selection, and follow-up care. The consortium was funded in September 2003. The investigators have collaboratively developed a core database and clinical protocols, and subject enrollment began in early 2005. A repository of data and biological specimens for future research also will be collected by the centers participating in LABS. These will provide valuable resources for future study of obesity and its complications.

Proper citation: Longitudinal Assessment of Bariatric Surgery (RRID:SCR_001536) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor software package for fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.

Proper citation: flowFP (RRID:SCR_001537) Copy   

•   Source: SciCrunch Registry

http://alfred.med.yale.edu

A public curated compilation of allele frequency data on anthropologically defined human population samples linked to the molecular genetics-human genome databases. Only data on well defined population samples that are large enough to yield reasonably accurate frequencies and for polymorphisms sufficiently defined to be replicable can be included in ALFRED. Researchers wishing to have their data entered into ALFRED should contact them. Initially, ALFRED contained primarily data generated in the laboratories of K.K. and J.R. Kidd in the Department of Genetics at Yale, including extensive unpublished data. Data from the published literature are being entered into ALFRED in a systematic way, with a focus on polymorphisms studied in many different populations. ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation. ALFRED's focus is on allele frequencies in diverse anthropologically defined populations. It is not a compendium of human DNA polymorphisms but of frequencies of selected polymorphisms with an emphasis on those that have been studied in multiple populations. All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching. ALFRED provides easy searching options including versatile "Keyword search" and also has numerous summary tables providing quick overviews of contents by chromosome, population, average heterozygosity, Fst and others, all available under various tabs from the ALFRED homepage.

Proper citation: ALFRED (RRID:SCR_001730) Copy   

•   Source: SciCrunch Registry

https://sbpdiscovery.org/tag/neuroscienceandagingresearchcenter/

Center that translates basic science discoveries into new treatments to extend lifespan and to combat degenerative disorders associated with aging or development. Their researchers are discovering the etiological pathways as well as small-molecule and stem cell-based treatments to address the clinical unmet need of these patients. The Center uses a team based approach to apply their expertise in stem cells to develop therapies for new treatments for stroke and Parkinson's disease. They are also performing high-throughput screens to identify new molecules to protect the synapses of nervesthe connections between nerves that mediate movement, memory and cognition for Alzheimer's, Parkinson's and autism. By studying the links between Down syndrome and Alzheimer's disease, they are exploring new treatments to improve cognition in both disorders. Their collaborations with clinical partners enable them to test new discoveries in human trials, with a goal to improve the lives of patients and families affected by neurodegenerative disease and aging disorders.

Proper citation: Sanford-Burnham Neuroscience and Aging Research Center (RRID:SCR_001688) Copy   

•   Source: SciCrunch Registry