Tools   Select Another Resource Report Type

https://github.com/SkywalkerLuke/TransHLA

Software tool to discern whether peptide will be recognized by HLA as epitope. Capable of directly identifying peptides as epitopes without the need for inputting HLA alleles. Hybrid transformer model for peptide-HLA epitope detection.

Proper citation: TransHLA (RRID:SCR_026171) Copy   

•   Source: SciCrunch Registry

https://admiramicro.com.mx

Core answers research questions in any scientific, medical or industrial discipline through capture, processing, image analysis, training and sample preparation services for microscopy. Provides technical and scientific support in advanced microscopy and image processing and analysis.

Proper citation: National Cancer Institute Advanced Microscopy Applications Unit Core Facility (RRID:SCR_026170) Copy   

•   Source: SciCrunch Registry

https://github.com/Greenbaum-Lab/bees.git

Software R code for analysis of social evolution in bees. Social complexity trait database and code. R scripts for analysis of bees evolution.

Proper citation: bees (RRID:SCR_026102) Copy   

•   Source: SciCrunch Registry

https://github.com/sahwa/ChromoPainterV2

Software tool to discover haplotypes in sequenced data. Colors each individual as hybrid of all other sequences. The "coancestry matrix" exposes ancestral associations among individuals. ChromoPainter algorithm uses Hidden Markov Model and outputs range of features, such as expected number of recombination events and sample haplotypes.

Proper citation: ChromoPainter (RRID:SCR_026062) Copy   

•   Source: SciCrunch Registry

http://biocc.hrbmu.edu.cn/CancerSEA/

Database that aims to comprehensively explore distinct functional states of cancer cells at the single-cell level. Provides functional state-associated PCG/lncRNA repertoires across all cancers, in specific cancers, and in individual cancer single-cell datasets. Provides interface for comprehensively searching, browsing, visualizing and downloading functional state activity profiles of cancer single cells and corresponding PCGs/lncRNAs expression profiles.

Proper citation: CancerSEA (RRID:SCR_026155) Copy   

•   Source: SciCrunch Registry

https://www.vai.org/research/collaborations/west-michigan-neurodegenerative-diseases-mind-program/

Brain bank that houses donated brains from people with neurodegenerative diseases and neurologically normal age-matched controls. VAI Brain Bank drives insight and discovery by providing scientists the samples needed to investigate the intricate underpinnings of Parkinson’s, dementias, and other neurodegenerative diseases.

Proper citation: Van Andel Institute Brain Bank (RRID:SCR_026035) Copy   

•   Source: SciCrunch Registry

https://github.com/Orin-beep/PlasGO

Software Python library (Linux or Ubuntu only) for predicting cluster level Gene Ontology terms of plasmid encoded proteins.

Proper citation: PlasGO (RRID:SCR_025983) Copy   

•   Source: SciCrunch Registry

https://sites.cscc.unc.edu/hchs/StudyOverview

Multi-center epidemiologic study in Hispanic/Latino populations to assess role of acculturation in prevalence and development of disease, and to identify factors playing protective or harmful role in health of Hispanics/Latinos.

Proper citation: Hispanic Community Health Study/Study of Latinos (RRID:SCR_026030) Copy   

•   Source: SciCrunch Registry

https://github.com/FridleyLab/spatialGE

Software R package for spatial analysis of spatial transcriptomics data. Used for visualization and analysis of spatially-resolved gene expression.

Proper citation: spatialGE (RRID:SCR_025979) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/CellBender

Software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing data. Deep generative model for noise removal in droplet-based single-cell RNA sequencing.

Proper citation: CellBender (RRID:SCR_025990) Copy   

•   Source: SciCrunch Registry

https://varsome.com/

Web service to search for variants, CNVs, genes, transcripts, publications, diseases. Annotation tool and search engine for human genomic variants, and platform enabling sharing of knowledge on specific variants. Enables users to look up variants in their genomic context, collects data from multiple databases in central location and most importantly, aims to enable community to freely and easily share knowledge on human variation.

Proper citation: VarSome (RRID:SCR_026165) Copy   

•   Source: SciCrunch Registry

https://www.hpa.gov.tw/Pages/TopicList.aspx?nodeid=649

Provides comprehensive national registry that systematically records all live births in Taiwan. It captures essential data on maternal and infant health, including maternal demographics, prenatal care, gestational age, birth weight, delivery method, and congenital anomalies. Established to facilitate public health monitoring and research, the TBRS enables studies on birth trends and outcomes, such as preterm birth and low birth weight, and provides a valuable resource for investigating the impacts of maternal health, environmental factors, and healthcare access on neonatal outcomes.TBRS database is instrumental in informing maternal and child health policies in Taiwan.

Proper citation: Taiwan Birth Reporting System Database (RRID:SCR_026047) Copy   

•   Source: SciCrunch Registry

https://themilolab.github.io/SPATA2/

Software package provides framework of functions and shiny-applications to work with spatial expression data. Used for spatial transcriptomics analysis.

Proper citation: SPATA2 (RRID:SCR_026167) Copy   

•   Source: SciCrunch Registry

https://dep.mohw.gov.tw/DOS/cp-5119-59201-113.html

Provides comprehensive dataset based on National Health Insurance program, which has covered over 99% of Taiwan's population since its launch in 1995. Database includes anonymized data on outpatient and inpatient visits, prescriptions, surgeries, diagnostics, and other medical information, ensuring individual privacy protection. NHI database is extensively utilized in fields such as public health, epidemiology, drug safety, and chronic disease monitoring, providing critical insights for research on major health conditions like cancer and cardiovascular diseases. Researchers use the NHIRD for long-term follow-up studies, treatment outcome analyses, and identifying disease risk factors, making it a valuable resource for healthcare policy and medical decision-making.

Proper citation: Taiwan National Health Insurance Database (RRID:SCR_026048) Copy   

•   Source: SciCrunch Registry

https://github.com/liulab-dfci/TRUST4

Software tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from fluid and solid tissues, including tumors. Performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 and reports consensus contigs of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to identify the corresponding gene and CDR3 details. TRUST4 supports both single-end and paired-end bulk or single-cell sequencing data with any read length.

Proper citation: TRUST4 (RRID:SCR_026162) Copy   

•   Source: SciCrunch Registry

https://yanglab.westlake.edu.cn/software/smr/

Software tool to test for pleiotropic association between expression level of gene and complex trait of interest using summary-level data from GWAS and expression quantitative trait loci eQTL studies. Used to prioritize genes underlying GWAS hits for follow up functional studies.

Proper citation: SMR (RRID:SCR_026042) Copy   

•   Source: SciCrunch Registry

https://github.com/theislab/destiny

Software R package for single cell and other data analysis using diffusion maps. Package for diffusion maps, with additional features for large-scale and single cell data.

Proper citation: Destiny (RRID:SCR_026163) Copy   

•   Source: SciCrunch Registry

https://johnshopkins.ilab.agilent.com/service_center/show_external/3819?name=reference-histology

Provides histology services for Autopsy, Cytology, Renal Pathology and Medical Archives Office within Department of Pathology. In conjunction with Pathology Send Out and Archives divisions, provides histology for clinical trial requests, scientific study or interest involving pathology materials. Services include: Complete routine paraffin histology services, including processing and sectioning; Special stains, including but not limited to carbohydrates, connective tissue, fats, lipids, microorganisms, nuclear elements, pigments, silver techniques; Immunopathology slide preparation techniques;DNA slide preparations; Frozen tissue sections; Oversized tissue processing and sectioning ;Histopathology teaching sets; Customized procedures.Services are provided for both human and animal tissue samples.

Proper citation: Johns Hopkins Reference Histology Core Facility (RRID:SCR_025986) Copy   

•   Source: SciCrunch Registry

https://github.com/susiegriggo/Phynteny

Software synteny-based tool for annotation of bacteriophage genes. Used to predict function of phage hypothetical proteins using LSTM model trained with Phage Synteny.

Proper citation: Phynteny (RRID:SCR_026015) Copy   

•   Source: SciCrunch Registry

https://chempartner.com/

Life sciences contract research organization. Provides integrated life science services for drug discovery with expertise in chemistry, biology and pharmacology, DMPK, and exploratory toxicology as well as biologics discovery.

Proper citation: ChemPartner (RRID:SCR_026139) Copy   

•   Source: SciCrunch Registry