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http://franklin.imgen.bcm.tmc.edu/

The mission of the Baylor College of Medicine - Shaw Laboratory is to apply methods of statistics and bioinformatics to the analysis of large scale genomic data. Our vision is data integration to reveal the underlying connections between genes and processes in order to cure disease and improve healthcare.

Proper citation: Baylor College of Medicine - Shaw Laboratory (RRID:SCR_000604) Copy   

•   Source: SciCrunch Registry
  

http://gdm.fmrp.usp.br/

Laboratory portal of the University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory.

Proper citation: USP Molecular Genetics and Bioinformatics Laboratory (RRID:SCR_000605) Copy   

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http://www.icmr.nic.in/

A government-funded council for the promotion and coordination of biomedical research in India. The council focuses on specific diseases such as HIV/AIDS, tuberculosis, and leprosy in addition to national health priorities including the management of communicable diseases, fertility control, and mental health research.

Proper citation: Indian Council of Medical Research; New Delhi; India (RRID:SCR_000968) Copy   

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http://biomed.med.miami.edu/

A department within the University of Miami which offers both undergraduate and postgraduate programs in neuroscience. The graduate program provides neuroscience research training in biological, behavioral, and physical sciences. This organization also conducts research through 55 active laboratories.

Proper citation: University of Miami, Department of Neuroscience (RRID:SCR_000723) Copy   

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http://www.fudan.edu.cn/en/

A public university in Shanghai, China that confers undergraduate and graduate degrees.

Proper citation: Fudan University; Shanghai; China (RRID:SCR_000965) Copy   

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http://www.bumc.bu.edu/cardiovascularproteomics/

The Cardiovascular Proteomics Center is a research center funded by the NIH/NHLBI to analyze and identify proteins that may be modified or created by oxidative stress. The CPC is developing and applying new proteomics methodology and instrumentation to the analysis of known proteins and those yet to be discovered.

Proper citation: Cardiovascular Proteomics Center (RRID:SCR_000603) Copy   

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http://skylign.org/

A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position.

Proper citation: Skylign (RRID:SCR_001176) Copy   

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https://rdrr.io/bioc/sRAP/

Software package that provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.

Proper citation: sRAP (RRID:SCR_001297) Copy   

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https://rdrr.io/bioc/yaqcaffy/

Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

Proper citation: yaqcaffy (RRID:SCR_001295) Copy   

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http://www.feinberg.northwestern.edu/

Medical school of Northwestern University which focuses on research initiatives, clinical affiliates, and global outlook.

Proper citation: Northwestern University Feinberg School of Medicine; Illinois; USA (RRID:SCR_001058) Copy   

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http://www.princeton.edu/

A private Ivy League research university based in New Jersey that confers undergraduate and graduate degrees in the humanities, social sciences, natural sciences, and engineering. It offers professional degrees in international affairs, engineering and applied science, architecture, and finance

Proper citation: Princeton University; New Jersey; USA (RRID:SCR_001059) Copy   

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http://www.medicine.uic.edu/

The medical school division of the University of Illinois with four separate campuses. The school focuses on excellence in research, education and clinical work, diversity and innovation, and collaboration.

Proper citation: University of Illinois College of Medicine; Illinois; USA (RRID:SCR_001057) Copy   

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

Software package that uses a modeling strategy especially designed for normalizing high-throughput genomic data. The premise is that your data is a function of study-specific variables which are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.

Proper citation: SNM (RRID:SCR_001299) Copy   

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http://montgomerylab.stanford.edu/spliceplot/index.html

A software tool for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files.

Proper citation: SplicePlot (RRID:SCR_001172) Copy   

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

Software package providing a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.

Proper citation: ChIPsim (RRID:SCR_001293) Copy   

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focuses on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data.

Proper citation: methyAnalysis (RRID:SCR_001290) Copy   

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https://github.com/Ensembl/WiggleTools

A multithreaded software library that computes statistics on large numbers of datasets, generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions.

Proper citation: WiggleTools (RRID:SCR_001170) Copy   

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http://julian-gehring.github.io/les/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.

Proper citation: les (RRID:SCR_001291) Copy   

•   Source: SciCrunch Registry
  

http://www.scienceexchange.com/facilities/4904

A contract research organization based in India that provides services including Clinical Development, Contract Manufacturing and Informatics.

Proper citation: GVK Biosciences Labs and Facilities (RRID:SCR_001044) Copy   

•   Source: SciCrunch Registry
  

http://purl.bioontology.org/ontology/BHO

An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.

Proper citation: Bleeding History Phenotype Ontology (RRID:SCR_001165) Copy   

•   Source: SciCrunch Registry