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http://www.bioconductor.org/

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

Proper citation: Bioconductor (RRID:SCR_006442) Copy   

•   Source: SciCrunch Registry

https://github.com/EpistasisLab/ReBATE

Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity .

Proper citation: ReBATE (RRID:SCR_017139) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/CHROMELEON7

Software system to support chromatography operations, to ensure data quality and manage all the analytical processes from instrument control, to raw data storage and processing, through to generating the final results.

Proper citation: Chromeleon Chromatography Data System (CDS) Software (RRID:SCR_016874) Copy   

•   Source: SciCrunch Registry

https://github.com/dorianps/LESYMAP

Software R package to conduct lesion-to-symptom mapping from human MRI data.Takes lesion maps and cognitive performance scores from patients with stroke, and maps brain areas responsible for cognitive deficit.

Proper citation: LESYMAP (RRID:SCR_017967) Copy   

•   Source: SciCrunch Registry

http://download.ant-neuro.com/matlab/

Software as an EEGLAB tool used for LIBEEP recordings.

Proper citation: Libeep EEGLAB plugin (RRID:SCR_016334) Copy   

•   Source: SciCrunch Registry

https://github.com/pachterlab/kb_python

Software Python package that wraps kallisto and bustools single-cell RNA-seq workflow. Used for single-cell RNA-seq pre-processing. Simplifies downloading and running of kallisto and bustools programs. Consists of kb ref and kb count commands. kb ref builds or downloads species specific index for pseudo alignment of reads and must be run prior to kb count and it runs kallisto index. kb count runs kallisto and bustools programs and is used for pre-processing of data from variety of single-cell RNA-seq technologies, and for number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.).

Proper citation: kb_python (RRID:SCR_018213) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/genomedata/

A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems.

Proper citation: Genomedata (RRID:SCR_004544) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000012a-2518-fb6c-5617-794280000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics.

Proper citation: Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center (RRID:SCR_009668) Copy   

•   Source: SciCrunch Registry

http://montana.eagle-i.net/i/0000012b-00be-4e65-df3b-3fdc80000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research.

Proper citation: Montana State University Bioinformatics Core Facility (RRID:SCR_009937) Copy   

•   Source: SciCrunch Registry

https://wistar.org/research-discoveries/shared-resources/bioinformatics-facility

Core provides High Throughput Data Analysis, Customized Bioinformatics Services, Custom Programming, High Performance Computing, Data management. Located in the Center for Systems and Computational Biology. Provides Cancer Center investigators with database management, software application support, expertise in statistical analyses and computational modeling of biomedical research data.

Proper citation: Wistar Bioinformatics Core Facility (RRID:SCR_010203) Copy   

•   Source: SciCrunch Registry

https://sdrc.stanford.edu/sdrc-research-cores/dctc/home/

With the following services from the Diabetes Clinical and Translational Core (DCTC), members will receive training in biospecimen preservation, study design, data analysis, data management, use of statistical software and clinical trial conduct.

Proper citation: Stanford Diabetes Research Center Diabetes Clinical and Translational Core (RRID:SCR_016212) Copy   

•   Source: SciCrunch Registry

https://sdrc.stanford.edu/sdrc-research-cores/dimc/home/

Core facility that provides immune monitoring assays at the RNA, protein, and cellular level, as well as archiving, reporting, and data mining support for clinical and translational studies related to Diabetes. The DIMC is a specialized subcore of the Human Immune Monitoring Center (HIMC) at Stanford.

Proper citation: Stanford Diabetes Research Center Diabetes Immune Monitoring Core (RRID:SCR_016210) Copy   

•   Source: SciCrunch Registry

https://voices.uchicago.edu/ucflow/

Core offers services in cytometry and antibody technology, helps to design projects, data acquisition, analysis and/or interpretation beyond routine practices,critical drafting and/or revision of manuscript for intellectual content purposes.

Proper citation: Chicago University Cytometry and Antibody Technology Core Facility (RRID:SCR_017760) Copy   

•   Source: SciCrunch Registry

http://mgm.ku.edu/services

Research oriented service laboratory providing informatics support to research community. Services include data analysis and mining in proteomics, genomics and chemistry, systems biology approaches such as pathway, network and interaction analyses, large scale statistical and machine learning studies, protein structure, function and stability prediction, sequence and domain analyses,d esign and implementation of relational databases and software programs, consultation on experimental design involving data acquisition, management and analysis, report, grant, and manuscript preparation.

Proper citation: Kansas University at Lawrence Applied Bioinformatics Laboratory Core Facility (RRID:SCR_017751) Copy   

•   Source: SciCrunch Registry

https://core.bioinformatics.udel.edu

CBCB Bioinformatics Data Science Core builds upon infrastructure of the Center for Bioinformatics and Computational Biology. Delaware Biotechnology Institute , Delaware Data Science Institute, and Protein Information Resource. Core helps with planning your research or analyzing your current data. Services:Consultation and Collaboration, Proposal Assistance,Training, Bioinformatics Software, Computational Hardware, Database and Web Services, Next Gen Analysis, Custom Analysis.

Proper citation: University of Delaware CBCB Bioinformatics Data Science Core Facility (RRID:SCR_017696) Copy   

•   Source: SciCrunch Registry

https://www.albany.edu/repr/

Resource offers range of mass spectrometry instrumentation, expertise in analysis of RNA, RNA modifications, and proteins involved in RNA metabolism/regulation, supports projects involving analysis of biomolecules, metabolites, and small synthetic molecules, provides consulting on experimental design, sample preparation and data interpretation, whole project development and grant writing contributions.

Proper citation: Albany University RNA Epitranscriptomics and Proteomics Resource Core Facility (RRID:SCR_017695) Copy   

•   Source: SciCrunch Registry

https://crc.ibest.uidaho.edu/

Provides evolutionary and computational biology investigators with computing and large data storage capacity for use in analyzing and managing large volumes of research data. Core contains advanced mix of high performance computing clusters, servers and data storage components, knowledge and technical skills required to compress years of analysis into days.

Proper citation: Idaho University IBEST Computational Resources Core Facility (RRID:SCR_017734) Copy   

•   Source: SciCrunch Registry

https://bioinformaticscore.unl.edu/bioinformatics-core-nebraska-center-virology

Facility is equipped with high performance computers, bioinformatics related software, biological databases, and data storage. Provides bioinformatics and computational services in virology, molecular biology, genomics, proteomics, next generation high throughput sequencing, and other biological related fields. For special requirements, can design and develop new algorithms, and implement programs and customize data processing pipelines. Core promotes education in bioinformatics to students and researchers, develops and delivers training material, including workshops that facilitate practical application of bioinformatics knowledge by students, postdoctoral fellows, and faculties in NCV community.

Proper citation: Nebraska-Lincoln University Center for Virology Bioinformatics Core Facility (RRID:SCR_017793) Copy   

•   Source: SciCrunch Registry

http://gif.biotech.iastate.edu/

Provides help with grant review, information on data management plans,suggestion best practices for bionformatics analyses, advise on experimental design for Next Gen Sequencing (NGS) projects.Services include:Genome assembly and annotation,Transcriptome assembly and annotation,SNP/InDel calling,RNA-Seq analysis,ChiP-seq,Introgression mapping,novel gene discovery,Personalized GBrowse instances for data visualization,Access to high performance computing, Custom big data projects.

Proper citation: Iowa State University Genome Informatics Core Facility (RRID:SCR_017790) Copy   

•   Source: SciCrunch Registry

https://www.une.edu/research/cobre/histology

Core provides access to expertise, training and specialized instrumentation related to tissue processing, sectioning, staining, immunohistochemistry and microscopy. Offers services and training related to image analysis and image analysis software to guide investigators in choosing best methods for presenting their data.Services include Trimming of wet tissues,Tissue processing into paraffin, OCT and paraffin embedding, Sectioning of paraffin-embedded/frozen tissues, Routine and special histochemical staining, Immunohistochemistry/Immunofluorescence, Antibody optimization, Brightfield/ widefield/ confocal microscopy, Image capture and image analysis.Core has cryostats, microtomes and microscopes available for reservation.

Proper citation: University of New England COBRE Histology and Imaging Core Facility (RRID:SCR_017885) Copy   

•   Source: SciCrunch Registry