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https://gtac.wustl.edu

Genome Access Technology Center at the McDonnell Genome Institute offers comprehensive next generation sequencing, microarray, PCR and Bioinformatic services. In addition to generating high quality genomic, transcriptomic, and proteomic data, performs data analysis and provides technological support to users. Full service facility, from hypothesis to publication. Offers advanced analysis of microarray data. Provides free initial consultation to discuss project and offers several tiers of analysis packages to best suit your needs. NGS equipment includes NovaSeqs, Seqwell II, Oxford. Microarray expression and genotyping - all platforms.

Proper citation: Washington University School of Medicine Genome Technology Access Center Core Facility (RRID:SCR_001030) Copy   

•   Source: SciCrunch Registry

http://pnabio.com

A company which provides peptide nucleic acid products for use in research. It also provides engineered nuclease services to laboratories.

Proper citation: PNA Bio (RRID:SCR_001037) Copy   

•   Source: SciCrunch Registry

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

Software package that facilitates comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

Proper citation: flowWorkspace (RRID:SCR_001155) Copy   

•   Source: SciCrunch Registry

http://www.renovoneural.com

A specialized preclinical research organization that provides services for biological research and development on neural therapies. Renovo offers preclinical assays and 3D-electron microscopy services that provide routine and customized solutions for basic science, preclinical and clinical research, and drug development.

Proper citation: Renovo Neural (RRID:SCR_001035) Copy   

•   Source: SciCrunch Registry

http://www.itk.org

Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

Proper citation: Insight Segmentation and Registration Toolkit (RRID:SCR_001149) Copy   

•   Source: SciCrunch Registry

http://131.174.198.125/bioinfo/gimmemotifs/

Software that provides a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GimmeMotifs (RRID:SCR_001146) Copy   

•   Source: SciCrunch Registry

https://immersive-analytics.infotech.monash.edu/vanted/

Software tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data.

Proper citation: Visualization and Analysis of Networks containing Experimental Data (VANTED) (RRID:SCR_001138) Copy   

•   Source: SciCrunch Registry

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

Software package that selects genes associated with survival.

Proper citation: rbsurv (RRID:SCR_001175) Copy   

•   Source: SciCrunch Registry

http://crossmap.sourceforge.net/

A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species.

Proper citation: CrossMap (RRID:SCR_001173) Copy   

•   Source: SciCrunch Registry

https://github.com/FelixKrueger/Sherman

Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments.

Proper citation: Sherman (RRID:SCR_001294) Copy   

•   Source: SciCrunch Registry

http://bioinf.scmb.uq.edu.au/STRViper/

Software tool for detection of short tandem repeat (STR) variations from paired-end next generation sequencing data. It makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats of size up to fragment length. This stratergy also helps avoiding false calls resulting from errors arised from sequencing of repeat DNA.

Proper citation: STRViper (RRID:SCR_001179) Copy   

•   Source: SciCrunch Registry

http://www.goldenhelix.com/GenomeBrowse/index.html

Software tool that delivers visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. A high performance backend is paired with an user interface to make sure that your discovery process is fluid and streamlined.

Proper citation: Golden Helix GenomeBrowse (RRID:SCR_001213) Copy   

•   Source: SciCrunch Registry

http://www.genome.duke.edu/labs/ohler/research/PARalyzer/

Software tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites.

Proper citation: PARalyzer (RRID:SCR_001208) Copy   

•   Source: SciCrunch Registry

http://heim.ifi.uio.no/bioinf/Projects/CGHExplorer/

Software program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion.

Proper citation: CGH-Explorer (RRID:SCR_001283) Copy   

•   Source: SciCrunch Registry

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

Software package providing a collection of meta-analysis tools for analysing high throughput experimental data.

Proper citation: GeneMeta (RRID:SCR_001201) Copy   

•   Source: SciCrunch Registry

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

Software package to detect different methylation levels (DMR) that gives the exact p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparison.

Proper citation: methylMnM (RRID:SCR_001289) Copy   

•   Source: SciCrunch Registry

http://www.merck.com/

An American pharmaceutical company aiming to make a difference in the lives of people globally through their medicines, vaccines, biologic therapies and animal health products.

Proper citation: Merck (RRID:SCR_001287) Copy   

•   Source: SciCrunch Registry

http://yiplab.cse.cuhk.edu.hk/probrna/

Software for computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.

Proper citation: ProbRNA (RRID:SCR_001288) Copy   

•   Source: SciCrunch Registry

http://cbcb.umd.edu/~hcorrada/secgen/

Software for ultra-fast base-calling of second-generation sequencing data by blind deconvolution.

Proper citation: BlindCall (RRID:SCR_001280) Copy   

•   Source: SciCrunch Registry

https://vcftools.github.io/index.html

Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API.

Proper citation: VCFtools (RRID:SCR_001235) Copy   

•   Source: SciCrunch Registry