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https://github.com/sanger-pathogens/Fastaq

Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together.

Proper citation: Fastaq (RRID:SCR_016091) Copy   

•   Source: SciCrunch Registry

https://www.urmc.rochester.edu/microbiology-immunology/xenopus-laevis.aspx

A comprehensive resource specializing in the use of the amphibian Xenopus laevis (the African clawed frog) for biomedical and immunological research. Several genetically-defined inbred strains and clones are available for study. The facility also maintains and develops research tools such as transgenic animals, monoclonal antibodies, cell lines, DNA libraries, and molecular probes. XLRR includes a satellite facility devoted to study infectious diseases caused by iridovirus. Technical assistance, education, and training are also provided.

Proper citation: Xenopus laevis Research Resource for Immunobiology (XLRR) (RRID:SCR_014354) Copy   

•   Source: SciCrunch Registry

https://www.med.upenn.edu/gtp/vectorcore/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. A full service viral vector core facility located at the University of Pennsylvania. This facility provides technological resources for investigators in their use of viral based vectors for gene transfer. The main objective of this core is to provide investigators with state-of-the-art vector technology for preclinical studies and other basic research applications, that will then increase understanding of gene function and the further development of therapeutic vectors.

Proper citation: Vector Core (RRID:SCR_014475) Copy   

•   Source: SciCrunch Registry

http://fastqtl.sourceforge.net/

Software for mapping of molecular phenotypes that implements a new permutation scheme to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels in large-scale datasets. It is used to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq.

Proper citation: Fastqtl (RRID:SCR_016093) Copy   

•   Source: SciCrunch Registry

http://gps.biocuckoo.org/

Software that detects kinase-specific phosphorylation sites. GPS provides a platform able to perform its prediction based on a group-based phosphorylation scoring algorithm. It allows users to query multiple protein sequences through a batch prediction mode.

Proper citation: GPS (RRID:SCR_016374) Copy   

•   Source: SciCrunch Registry

http://harvest.readthedocs.org/en/latest/content/harvest-tools.html

Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations.

Proper citation: Harvest-tools (RRID:SCR_016132) Copy   

•   Source: SciCrunch Registry

http://www.moldiscovery.com/software/vsplus/

Software package for molecular descriptors, ADME prediction and membrane permeability prediction. These can then be used with provided chemometric tools to build statistical models.

Proper citation: VolSurf (RRID:SCR_014911) Copy   

•   Source: SciCrunch Registry

http://www.uchicagoddrcc.org/research-cores/tissue-engineering-and-cell-models-core

Core that provides services such as a repository for intestinal cell lines, Tissue Engineering Models, experimental materials, and supplies for digestive disease research.

Proper citation: University of Chicago Digestive Diseases Research Core Center Tissue Engineering and Cell Models Core (RRID:SCR_015604) Copy   

•   Source: SciCrunch Registry

http://huttenhower.sph.harvard.edu/galaxy

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LEfSe (RRID:SCR_014609) Copy   

•   Source: SciCrunch Registry

http://CRAN.R-project.org/package=RVAideMemoire

Software package that contains miscellaneous functions useful in biostatistics, such as univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions shorten existing procedures and implement plotting functions that can be used with a variety of methods and packages.

Proper citation: R package: RVAideMemoire (RRID:SCR_015657) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/media-preparation-core/

Core facility that provides media, plates, and commonly used buffers for molecular biology applications and culturing mammalian cells, C. elegans, yeast, and bacteria. The Media Preparation Core Facility is equipped with 3 automatic plate pourers supported by 2 programmable media kettles capable of producing up to 9 liters of agar or nutrient media per run under gentle and reproducible conditions. Plates are available in 6 cm or 10 cm formats.

Proper citation: Salk Institute Media Preparation Core Facility (MPRP) (RRID:SCR_014844) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=Boruta

Algorithm that performs feature selection. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).

Proper citation: Boruta (RRID:SCR_016234) Copy   

•   Source: SciCrunch Registry

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

Software R package for estimating structural equation models using instrumental variables.

Proper citation: MIIVsem (RRID:SCR_017444) 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/lrq3000/spm_auto_reorient_coregister

Open source cross platform for automatic AC-PC realignment, reorientation and coregistration robust to brain damage in Statistical Parametric Mapping. Set of routines to perform auto reorient and auto coregistration in toolbox SPM12.

Proper citation: spm_auto_reorient_coregister (RRID:SCR_017281) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_StemCells.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The former functions of this facility are split into two separate operations. The first is the generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators with the Snyder lab. The second is a shared laboratory dedicated to the culture and analysis of stem cells that is available to SBP investigators.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core (RRID:SCR_014856) Copy   

•   Source: SciCrunch Registry

https://github.com/QTIM-Lab/DeepNeuro

Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners.

Proper citation: DeepNeuro (RRID:SCR_016911) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_TumorAnalysis.aspx

Facility that provides analysis of animal models of human cancer and other diseases. It provides investigators access to a wide variety of human cancer cell lines for xenograft studies, some primary human xenograft models and additional transgenic mouse solid tumors and leukemia models. The core also offers serial passaging of tumors and derivation of 2D and 3D cultures from xenograft tumors, including patient-derived xenograft (PDX) models. These short-term cell cultures established from PDXs enable in vitro analysis including high throughput screening with compounds or RNAi for functional characterization.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Tumor Analysis (RRID:SCR_014858) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/dti-denoising/

A Matlab package which contains six denoising filters and a noise estimation method for 4D DWI. The package includes nonlocal means, local PCA and Oracle DCT methods. Based on image redundancy and/or sparsity, the proposed filters provide efficient denoising while preserving fine structures.

Proper citation: DTI denoising (RRID:SCR_014102) Copy   

•   Source: SciCrunch Registry

https://github.com/missy139/PreSurgMapp

A MATLAB toolbox for processing the functional areas of the brain using multi-modal fMRI data for pre-surgical mapping. It is composed of three types of individual-level ICA analyses for user use. Traditional ICA (task) can be used for task fMRI. Either Traditional ICA (rest) or ICA with DICI (rest) can be used for rs-fMRI. Traditional ICA (rest) is designed for users who already have a hypothesis of the pattern of the target component and want to have manually set components by themselves. ICA with DICI (rest) is completely automatic, given that the user provides a template (provided). The software utilizes an automatic component identification method that is based on the discriminatory-index. All the components from multiple ICA runs with multiple component settings are ranked and compiled.

Proper citation: PreSurgMapp (RRID:SCR_014427) Copy   

•   Source: SciCrunch Registry