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http://www.medschool.vcu.edu/

Medical school division of Virginia Commonwealth University.

Proper citation: Virginia Commonwealth University School of Medicine; Virginia; USA (RRID:SCR_001061) Copy   

•   Source: SciCrunch Registry

http://www.ed.gov/

The United States federal government Department of Education, which oversees policies on federal financial aid for education, collecting data and disseminating research, and working to promote key educational discussions and equal access to education.

Proper citation: U.S. Department of Education (RRID:SCR_001060) Copy   

•   Source: SciCrunch Registry

https://omictools.com/npebseq-tool

A method for non-parametric, empirical Bayesian-based analysis of RNA-seq count data.

Proper citation: NPEBseq (RRID:SCR_001014) Copy   

•   Source: SciCrunch Registry

https://www.hytest.fi/home

A commercial antibody supplier that specializes in high-quality monoclonal antibodies and antigens for the diagnostic industry.

Proper citation: Hytest (RRID:SCR_001133) Copy   

•   Source: SciCrunch Registry

http://www.stat.brown.edu/ZWU/research.aspx

Borrows information across sequences to establish prior distribution of sample variation, so that biological variation can be accounted for even when replicates are not available.

Proper citation: ASC (RRID:SCR_001013) Copy   

•   Source: SciCrunch Registry

http://www.biolegend.com/

Commercial antibody supplier and developer for biomedical research. These products are compatible with use in flow cytometry and mass cytometry, immunoprecipitation and chip, western blotting, immunofluorescence microscopy, and quantitative multiplexing.

Proper citation: BioLegend (RRID:SCR_001134) Copy   

•   Source: SciCrunch Registry

http://www.neweastbio.com/

Commercial supplier which provides antibodies, assay kits, biomarkers, and proteins.

Proper citation: NewEast Biosciences (RRID:SCR_001129) Copy   

•   Source: SciCrunch Registry

http://www.utah.edu/

Public university in Utah, USA that provides undergraduate, master's, post graduate, graduate, and professional degree programs.

Proper citation: University of Utah; Utah; USA (RRID:SCR_001003) Copy   

•   Source: SciCrunch Registry

http://www.howard.edu/

A federally chartered, private, coeducational, nonsectarian, historically black university in Washington, D.C. Howard University has graduate schools in many fields, including business, nursing, engineering, and medicine.

Proper citation: Howard University; Washington D.C. (RRID:SCR_001084) Copy   

•   Source: SciCrunch Registry

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

A Java application programming interface (API) for the Proteomics Standards Initiative mzML data standard.

Proper citation: jmzML (RRID:SCR_001119) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/devel/bioc/html/massiR.html

Software that predicts the sex of samples in gene expression microarray datasets.

Proper citation: massiR (RRID:SCR_001157) Copy   

•   Source: SciCrunch Registry

https://www.phoenixpeptide.com/

Commercial antibody supplier that specializes in peptide-related products for research in obesity, cardiovascular disease, and diabetes.

Proper citation: Phoenix Pharmaceuticals (RRID:SCR_001141) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/~stijn/reaper/reaper.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. Software program for demultiplexing, trimming and filtering short read sequencing data.

Proper citation: Reaper - Demultiplexing trimming and filtering sequencing data (RRID:SCR_001144) Copy   

•   Source: SciCrunch Registry

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

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   

•   Source: SciCrunch Registry

http://122.228.158.106/BSSim/

Software to mimic various methylation level and bisulfite conversion rate in CpG, CHG and CHH context, respectively. It can also simulate genetic variations that are divergent from the reference sequence along with the sequencing error and quality distributions. In the output, both directional/non-directional, various read length, single/paired-end reads and alignment data in the SAM format can be generated. BSSim is a cross-platform BS-seq simulator offers output read datasets not only suitable for Illumina's Solexa, but also for Roche's 454 and Applied Biosystems' SOLiD.

Proper citation: BSSim (RRID:SCR_001212) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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://qualimap.bioinfo.cipf.es/

Software application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. It examines sequencing alignment data in SAM / BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.

Proper citation: QualiMap (RRID:SCR_001209) Copy   

•   Source: SciCrunch Registry