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http://interactome.baderlab.org/

Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies.

Proper citation: Human Reference Protein Interactome Project (RRID:SCR_015670) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/cancer/cga/polysolver

Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference.

Proper citation: Polysolver (RRID:SCR_022278) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/sigcom-lincs

Web server that serves over million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. Data and metadata search engine for gene expression signatures.

Proper citation: SigCom LINCS (RRID:SCR_022275) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/pmlb/

Python wrapper for Penn Machine Learning Benchmark data repository. Large, curated repository of benchmark datasets for evaluating supervised machine learning algorithms. Part of PyPI https://pypi.org/

Proper citation: Penn machine learning benchmark repository (RRID:SCR_017138) Copy   

•   Source: SciCrunch Registry

https://www.signalingpathways.org/ominer/query.jsf

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 25, 2022.Software tool as knowledge environment resource that accrues, develops, and communicates information that advances understanding of structure, function, and role in disease of nuclear receptors (NRs) and coregulators. It specifically seeks to elucidate roles played by NRs and coregulators in metabolism and development of metabolic disorders. Includes large validated data sets, access to reagents, new findings, library of annotated prior publications in field, and journal covering reviews and techniques.As of March 20, 2020, NURSA is succeeded by the Signaling Pathways Project (SPP).

Proper citation: Nuclear Receptor Signaling Atlas (RRID:SCR_003287) Copy   

•   Source: SciCrunch Registry

https://www.ngvbcc.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Archiving services, insertional site analysis, pharmacology and toxicology resources, and reagent repository for academic investigators and others conducting gene therapy research. Databases and educational resources are open to everyone. Other services are limited to gene therapy investigators working in academic or other non-profit organizations. Stores reserve or back-up clinical grade vector and master cell banks. Maintains samples from any gene therapy related Pharmacology or Toxicology study that has been submitted to FDA by U.S. academic investigator that require storage under Good Laboratory Practices. For certain gene therapy clinical trials, FDA has required post-trial monitoring of patients, evaluating clinical samples for evidence of clonal expansion of cells. To help academic investigators comply with this FDA recommendation, the NGVB offers assistance with clonal analysis using LAM-PCR and LM-PCR technology.

Proper citation: National Gene Vector Biorepository (RRID:SCR_004760) Copy   

•   Source: SciCrunch Registry

http://snyderome.stanford.edu/

Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions.

Proper citation: iPOP (RRID:SCR_008991) Copy   

•   Source: SciCrunch Registry

https://github.com/FunctionLab/sei-framework

Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types.

Proper citation: sei (RRID:SCR_022571) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/X2K

Web service to predict involvement of upstream cell signaling pathways, given signature of differentially expressed genes. Used to linking expression signatures to upstream cell signaling networks.

Proper citation: X2K Web (RRID:SCR_023624) Copy   

•   Source: SciCrunch Registry

https://pmc.ncbi.nlm.nih.gov/articles/PMC4525701/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 25,2025. Web tool to parse Sanger sequencing chromatograms with double peaks into wildtype and alternative allele sequences. Used to separate chromatogram data containing ambiguous base calls into wildtype and mutant allele sequences.Used for identification of unknown indels using sanger sequencing of polymerase chain reaction products.

Proper citation: Poly Peak Parser (RRID:SCR_023776) Copy   

•   Source: SciCrunch Registry

https://github.com/humanlongevity/HLA

Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer.

Proper citation: xHLA (RRID:SCR_022277) Copy   

•   Source: SciCrunch Registry

https://lincsportal.ccs.miami.edu/signatures/home

Primary access point for compendium of LINCS data with substantial changes in data architecture and APIs, completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. LINCS datasets are accessible at data point level enabling users to directly access and download any subset of signatures across entire library independent from originating source, project or assay. Newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures.

Proper citation: LINCS Data Portal 2.0 (RRID:SCR_022566) Copy   

•   Source: SciCrunch Registry

http://www.nhlbi.nih.gov/guidelines/obesity/BMI/bmicalc.htm

Body Mass Index (BMI) for adults can be calculated using only height and weight. Body mass index (BMI) is a measure of body fat based on height and weight that applies to adult men and women.

Proper citation: Body Mass Index Calculator (RRID:SCR_000122) Copy   

•   Source: SciCrunch Registry

http://proteomics.ucsd.edu/Software/NeuroPedia/index.html

A neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species.

Proper citation: NeuroPedia (RRID:SCR_001551) Copy   

•   Source: SciCrunch Registry

http://www.uniprot.org/

Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

Proper citation: UniProt (RRID:SCR_002380) Copy   

•   Source: SciCrunch Registry

http://www.cycif.org/

Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence.

Proper citation: CycIF.org (RRID:SCR_016267) Copy   

•   Source: SciCrunch Registry

https://hub.docker.com/r/biodepot/star-for-criu/

Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability.

Proper citation: star-for-criu (RRID:SCR_016294) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/LJP/

Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations.

Proper citation: LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/datasets/shhs

Portal for a multi-cohort study focused on sleep-disordered breathing and cardiovascular outcomes implemented by the National Heart Lung and Blood Institute. Recorded signals are: EEG, ECG, EOG, SaO2, HR, EOG, EMG, respiratory inductance plethysmography, respiration (thermistor), position, light.

Proper citation: Sleep Heart Health Study (RRID:SCR_016559) Copy   

•   Source: SciCrunch Registry

https://github.com/xu-lab/SINCERA

Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis.

Proper citation: SINCERA Pipeline (RRID:SCR_016563) Copy   

•   Source: SciCrunch Registry