Tools   Select Another Resource Report Type

https://www.fil.ion.ucl.ac.uk/spm/ext/#TSDiffAna

Software tool developed for Statistical Parametric Mapping (SPM) that computes slicewise scan by scan difference and standard deviations. Used to examine quality of image timeseries.

Proper citation: TSDiffAna (RRID:SCR_016656) Copy   

•   Source: SciCrunch Registry

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

Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems.

Proper citation: Nutil - Neuroimaging utilities (RRID:SCR_017183) Copy   

•   Source: SciCrunch Registry

https://kidsfirstdrc.org/portal/portal-features/

Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects.

Proper citation: Kids First Data Resource Portal (RRID:SCR_016493) Copy   

•   Source: SciCrunch Registry

https://nephele.niaid.nih.gov

Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools.

Proper citation: Nephele (RRID:SCR_016595) Copy   

•   Source: SciCrunch Registry

http://www.cyflogic.com/

Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics.

Proper citation: Cyflogic (RRID:SCR_016635) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/sutils/pasc/viridty.cgi

Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database.

Proper citation: PASC (RRID:SCR_016642) Copy   

•   Source: SciCrunch Registry

http://ccg.vital-it.ch/snp2tfbs

Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs.

Proper citation: SNP2TFBS (RRID:SCR_016885) Copy   

•   Source: SciCrunch Registry

http://home.cc.umanitoba.ca/~frist/Bit/

BIT Core at University of Manitoba, Manitoba, Canada, provides bioinformatics services, resources and collaborations. Support for Genome assembly and annotation, Microarray and Transcriptomics, Systems Biology and Pathway analysis, Databases, Data pipelines, Bioinformatics software, Custom software and programming, Project Wikis, Lab group computer management.

Proper citation: University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility (RRID:SCR_017177) Copy   

•   Source: SciCrunch Registry

http://hpc-bioinformatics.cineca.it/stress_mice/

Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data.

Proper citation: Stress Mice Portal (RRID:SCR_017572) Copy   

•   Source: SciCrunch Registry

https://omicc.niaid.nih.gov

Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: OMiCC (RRID:SCR_016604) Copy   

•   Source: SciCrunch Registry

https://github.com/wilkinsonlab/epigenomics_pipeline

Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter.

Proper citation: Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) Copy   

•   Source: SciCrunch Registry

https://opticalmapping.info

Platform to provide tutorials and resources in experimental design and data analysis to researchers interested in using optical mapping data.

Proper citation: OpticalMapping.info (RRID:SCR_017146) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/factoextra/index.html

R package from CRAN to extract and visualize the results of multivariate data analysis.

Proper citation: factoextra (RRID:SCR_016692) Copy   

•   Source: SciCrunch Registry

https://github.com/sreeramkannan/Shannon

Software tool for de novo transcriptome assembly from RNA-Seq data.

Proper citation: Shannon (RRID:SCR_017037) Copy   

•   Source: SciCrunch Registry

https://github.com/neurostuff/NiMARE

Software Python package for coordinate and image based meta analysis of neuroimaging data.

Proper citation: NiMARE (RRID:SCR_017398) Copy   

•   Source: SciCrunch Registry

https://www.iconplc.com/innovation/nonmem/

Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions.

Proper citation: NONMEM (RRID:SCR_016986) Copy   

•   Source: SciCrunch Registry

https://github.com/ANGSD/ngsRelate

Software tool for estimating pairwise relatedness from next-generation sequencing data.

Proper citation: ngsRelate (RRID:SCR_016588) Copy   

•   Source: SciCrunch Registry

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

Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns.

Proper citation: ComplexHeatmap (RRID:SCR_017270) Copy   

•   Source: SciCrunch Registry

http://redrocksw.com/

Software tool for statistics and data visualization by Red Rock Software, Inc. Provides unparalleled chart selection, data analysis and graph customization capabilities.

Proper citation: Deltagraph (RRID:SCR_018084) Copy   

•   Source: SciCrunch Registry

https://satijalab.org/seurat/get_started.html

Software as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.

Proper citation: Seurat (RRID:SCR_016341) Copy   

•   Source: SciCrunch Registry