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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://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

http://cleversysinc.com/CleverSysInc/?csi_products=topscan-suite

Software suite as top view based behavior analysis system by CleverSys Inc. Uses animal body parts to provide behavior analysis results. Used in experiments with animal tracking task.

Proper citation: TopScan (RRID:SCR_017141) Copy   

•   Source: SciCrunch Registry

http://hibberdlab.com/transrate/

Open source software tool for de novo transcriptome assembly reference free quality analysis. Used to examine assembly in detail and compare it to sequencing reads, reporting quality scores for contigs and assemblies to allow to choose between assemblers and parameters, filter out bad contigs from an assembly, and help decide when to stop trying to improve assembly.

Proper citation: TransRate (RRID:SCR_017034) 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/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

https://bibiserv.cebitec.uni-bielefeld.de/pkiss

Software tool for folding RNA secondary structures, including two limited classes of pseudoknots. Performs abstract shape analysis for structures holding pseudoknots up to complexity of kissing hairpin motifs. Successor of pknotsRG. Used for secondary structure prediction including kissing hairpin motifs.

Proper citation: pKiss (RRID:SCR_017256) Copy   

•   Source: SciCrunch Registry

http://research.mssm.edu/integrative-network-biology/Software.html

Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles.

Proper citation: proMODMatcher (RRID:SCR_017219) Copy   

•   Source: SciCrunch Registry

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

Software tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics.

Proper citation: Cell Ranger (RRID:SCR_017344) Copy   

•   Source: SciCrunch Registry

https://github.com/aidenlab/juicer.git

Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps.

Proper citation: Juicer (RRID:SCR_017226) Copy   

•   Source: SciCrunch Registry

http://snf-515788.vm.okeanos.grnet.gr/

Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DIANA-mirPath (RRID:SCR_017354) Copy   

•   Source: SciCrunch Registry

http://pathwaynet.princeton.edu/

Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.

Proper citation: PathwayNet (RRID:SCR_017353) Copy   

•   Source: SciCrunch Registry

https://www.keyence.co.jp/products/microscope/fluorescence-microscope/bz-8100/models/bz-h1a/

Software tool as analysis application BZ-H1A by Keyence, Japan for fluorescence microscope BZ-8100 series.

Proper citation: BZ Analyzer software (RRID:SCR_017205) Copy   

•   Source: SciCrunch Registry

http://relacs.sourceforge.net/

Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings.

Proper citation: Relacs (RRID:SCR_017280) Copy   

•   Source: SciCrunch Registry