Tools   Select Another Resource Report Type

http://hlathena.tools/

Web tool and predictive model used by researchers to identify which small protein fragments (peptides) will be presented by human leukocyte antigen (HLA) proteins on the surface of cells. It is heavily used in the development of cancer immunotherapies and personalized

Proper citation: HLAthena (RRID:SCR_028691) Copy   

•   Source: SciCrunch Registry

https://crispresso.pinellolab.partners.org/submission

Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments.

Proper citation: CRISPResso (RRID:SCR_021538) Copy   

•   Source: SciCrunch Registry

http://www.nsrrc.missouri.edu/

Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research.

Proper citation: National Swine Resource and Research Center (RRID:SCR_006855) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

Proper citation: Synapse (RRID:SCR_006307) Copy   

•   Source: SciCrunch Registry

http://pepr.cnmcresearch.org/

An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ).

Proper citation: Public Expression Profiling Resource (RRID:SCR_007274) Copy   

•   Source: SciCrunch Registry

http://www.scandb.org/newinterface/about.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SCAN (RRID:SCR_005185) Copy   

•   Source: SciCrunch Registry

https://biolincc.nhlbi.nih.gov/home/

Repository that serves to coordinate searches across data and biospecimen collections from participants in numerous clinical trials and epidemiologic studies and to provide an electronic means for requests for additional information and the submission of requests for collections. The collections, comprising data from more than 80 trials or studies and millions of biospecimens, are available to qualified investigators under specific terms and conditions consistent with the informed consents provided by the individual study participants. Some datasets are presented with studies and supporting materials to facilitate their use in reuse and teaching. Datasets support basic research, clinical studies, observational studies, and demonstrations. Researchers wishing to apply to submit biospecimen collections to the NHLBI Biorepository for sharing with qualified investigators may also use this website to initiate that process.

Proper citation: Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) (RRID:SCR_013142) Copy   

•   Source: SciCrunch Registry

http://hb.flatironinstitute.org/

Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations.

Proper citation: HumanBase (RRID:SCR_016145) Copy   

•   Source: SciCrunch Registry

https://signalingpathways.org

Web multi omics knowledgebase based upon public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Integrated omics knowledgebase for mammalian cellular signaling pathways. Web browser interface was designed to accommodate numerous routine data mining strategies. Datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available.

Proper citation: Signaling Pathways Project (RRID:SCR_018412) Copy   

•   Source: SciCrunch Registry

https://github.com/rondolab/MR-PRESSO

Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing.

Proper citation: MR-PRESSO (RRID:SCR_023697) Copy   

•   Source: SciCrunch Registry

http://pipeline.lbl.gov/cgi-bin/gateway2

Software tools for comparative genomics.Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.

Proper citation: VISTA Browser (RRID:SCR_011808) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/SingleR.html

Software R package for unbiased cell type recognition of scRNA-seq data. Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer cell of origin of each single cell independently.

Proper citation: SingleR (RRID:SCR_023120) Copy   

•   Source: SciCrunch Registry

https://reprint-apms.org/?q=chooseworkflow

Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions.

Proper citation: CRAPome (RRID:SCR_025008) Copy   

•   Source: SciCrunch Registry

https://github.com/sxf296/drug_targeting

Software tool to detect phenotypically relevant drug targets through unique transcriptomic enrichment that emphasizes biological directionality of drug-derived gene sets. Exploratory tool to screen for possible drug targeting molecules.

Proper citation: drug perturbation Gene Set Enrichment Analysis (RRID:SCR_025351) Copy   

•   Source: SciCrunch Registry

https://github.com/GregorySchwartz/too-many-cells

Software suite of tools, algorithms, and visualizations focusing on relationships between cell clades. This includes new ways of clustering, plotting, choosing differential expression comparisons. Identifies and visualizes relationships of single-cell clades.

Proper citation: TooManyCells (RRID:SCR_025328) Copy   

•   Source: SciCrunch Registry

https://predictomes.org/

Interactive database of protein protein interactions modeled by AlphaFold multimer. Classifier-curated database of AlphaFold-modeled protein-protein interactions.

Proper citation: Predictomes (RRID:SCR_026691) Copy   

•   Source: SciCrunch Registry

https://github.com/calico/borzoi

Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences.

Proper citation: Borzoi (RRID:SCR_026619) Copy   

•   Source: SciCrunch Registry

https://github.com/QuackenbushLab/NetworkDataCompanion

Software R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo. Streamlines routine steps in TCGA data processing, including filtering and mapping gene and sample identifiers between modalities and allows modality-specific data transformation, such as normalization and cleaning.

Proper citation: NetworkDataCompanion (RRID:SCR_026532) Copy   

•   Source: SciCrunch Registry

https://github.com/williamslab/ped-sim

Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances.

Proper citation: ped-sim (RRID:SCR_026957) Copy   

•   Source: SciCrunch Registry