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http://mayoresearch.mayo.edu/mayo/research/biostat/index.cfm

Core assists in genomics, proteomics and metabolomics data acquisition, management, analyses and interpretation to Mayo investigators. Participates in Basic science research, Clinical trials, Population health, and Translational science to execute analytical workflows and manage large omics data sets. Provides support to Mayo Clinic Center for Individualized Medicine and Mayo Clinic Cancer Center. Has its academic home in Department of Health Sciences Research within Division of Biomedical Statistics and Informatics.

Proper citation: Mayo Clinic Rochehster Bioinformatics Core Facility (RRID:SCR_017161) Copy   

•   Source: SciCrunch Registry

https://www.ie-freiburg.mpg.de/bioinformaticsfac

Core provides assistance in primary analysis of sequencing data and other large scale biocomputing. For our internal users we host extensive web services, workflows and customized tools that help with data management, visualizations, standardized analyses and data sharing.

Proper citation: Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility (RRID:SCR_017160) Copy   

•   Source: SciCrunch Registry

https://github.com/dgrun/RaceID

Algorithm for identification of rare and abundant cell types from single cell transcriptome data. Based on transcript counts obtained with unique molecular identifies. Used for discovering rare cell types and corresponding marker genes in healthy and diseased organs. Operating system Unix/Linux, Mac OS, Windows.

Proper citation: RaceID (RRID:SCR_017045) Copy   

•   Source: SciCrunch Registry

https://medicine.umich.edu/dept/dcmb/center-computational-medicine-bioinformatics

University interdisciplinary academic center for bioinformatics, biomedical data science, and translational precision health informatics. Core provides training programs.

Proper citation: University of Michigan School of Medicine Center of Computational Medicine and Bioinformatics Core Facility (RRID:SCR_017179) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/goseq.html

Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies.

Proper citation: Goseq (RRID:SCR_017052) Copy   

•   Source: SciCrunch Registry

https://www.medsci.ox.ac.uk/research/labtalk/labtalk

Core provides genomics training, as well as assistance in next generation sequencing analyses.

Proper citation: University of Oxford Medical Sciences Division Computational Genomics: Analysis and Training Core Facility (RRID:SCR_017173) Copy   

•   Source: SciCrunch Registry

https://ircm.qc.ca/en/technological-services/bioinformatics

Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses.

Proper citation: Montreal Clinical Research Bioinformatics Core Facility (RRID:SCR_017176) Copy   

•   Source: SciCrunch Registry

https://git.ufz.de/iTox/toxprofileR

Software R package to derive toxicogenomic fingerprints from microarray data.

Proper citation: toxprofileR (RRID:SCR_017027) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com/en/products/software-informatics/masshunter-suite/masshunter-for-life-science-research/profinder-software

Software tool as fast, batch processing feature extraction software for differential analysis that supports data from Agilent GC/MSD, GC/Q-TOF, LC/TOF and LC/Q-TOF instruments. Speeds up differential and flux analysis workflows using intuitive user interface. Used to analyze raw mass spectrometry data, choose peaks.

Proper citation: Profinder (RRID:SCR_017026) Copy   

•   Source: SciCrunch Registry

https://biocore.crg.eu/wiki/Main_Page

Provides services of consultation and data analysis, with focus on Next Generation Sequencing and other high throughput experiments, software and database development, and training in basic and advanced bioinformatics techniques. Services provided for fee to support collaborative grant funded investigations.

Proper citation: Centre for Genome Regulation Bioinformatics Core Facility (RRID:SCR_017145) Copy   

•   Source: SciCrunch Registry

https://www.bruker.com/pt/products/mr/epr/epr-software/winepr/overview.html

Software tool to operate the EMX series of spectrometers by Bruker. Provides rapid data analysis of 1D and 2D data sets, provides environment for acquisition and processing of CW-EPR and CW-ENDOR spectra with the EMXplus and EMXmicro series of spectrometers.

Proper citation: Bruker WinEPR program (RRID:SCR_017023) Copy   

•   Source: SciCrunch Registry

https://github.com/aldenleung/OMTools

Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles.

Proper citation: OMTools (RRID:SCR_017143) Copy   

•   Source: SciCrunch Registry

https://combine-lab.github.io/salmon/

Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias.

Proper citation: Salmon (RRID:SCR_017036) Copy   

•   Source: SciCrunch Registry

https://github.com/fmaguire/Bridger_Assembler

Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.

Proper citation: Bridger (RRID:SCR_017039) Copy   

•   Source: SciCrunch Registry

https://pcago.bioinf.uni-jena.de/

Interactive web service for analysis of RNA-Seq read count data with principal component analysis (PCA) and agglomerative clustering. Includes features like read count normalization, filtering read counts by gene annotation and visualization options.

Proper citation: PCAGO (RRID:SCR_017033) Copy   

•   Source: SciCrunch Registry

https://github.com/dgrun/FateID

Software R package for inference of cell fate bias from single cell RNA-seq data. Iterative supervised learning algorithm for probabilistic quantification of cell fate bias in progenitor populations.

Proper citation: FateID (RRID:SCR_017244) Copy   

•   Source: SciCrunch Registry

https://github.com/jefferis/nat

Software R package for 3D visualisation and analysis of biological image data, especially tracings of single neurons.

Proper citation: NeuroAnatomy Toolbox (RRID:SCR_017248) Copy   

•   Source: SciCrunch Registry

https://github.com/powellgenomicslab/ascend

Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions.

Proper citation: ascend (RRID:SCR_017257) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/vini/

Software Python tool as viewer for MRI data and numpy arrays.

Proper citation: vini: A viewer for fMRI data (RRID:SCR_017250) Copy   

•   Source: SciCrunch Registry

http://www.iqtree.org/

Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference.

Proper citation: IQ-TREE (RRID:SCR_017254) Copy   

•   Source: SciCrunch Registry