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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Harmonized DRG and TG Reference Atlas Resource Report Resource Website 1+ mentions |
Harmonized DRG and TG Reference Atlas (RRID:SCR_025720) | data or information resource, reference atlas, software resource, source code, atlas | Harmonized cell atlases using sc/snRNA-seq data obtained from dorsal root ganglia and trigeminal ganglio mammalian datasets. | Harmonized cell atlas, peripheral nervous system, RNA-Seq, dorsal root ganglion, trigeminal ganglia, | is related to: NIH PRECISION Human Pain Network | Pain | Burroughs Wellcome Fund ; Rita Allen Foundation ; Migraine Research Foundation ; Edwards PhD Studentship in Pain Research ; Barry Family Harvard Stem Cell Institute Award ; NINDS U19NS130617; NINDS R01NS119476; NINDS U19NS130608; NINDS U19NS130607; NIDA DP1DA054343; NEI U01EY034709; Teva Pharmaceuticals ; BWH Women’s Brain Initiative ; BWH Neurotechnology Studio ; MGB Gene and Cell Therapy Institute |
DOI:10.1126/sciadv.adj9173 | Free, Freely available | https://github.com/Renthal-Lab/harmonized_atlas | SCR_025720 | 2026-08-14 09:29:43 | 4 | ||||||
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UTHealth Houston Center for Advanced Microscopy Core Facility Resource Report Resource Website 10+ mentions |
UTHealth Houston Center for Advanced Microscopy Core Facility (RRID:SCR_025962) | service resource, access service resource, core facility | Microscopy facility serving Texas Medical Center. Facilitates utilization of advanced light microscopy techniques and quantitative image analysis to advance research programs of McGovern Medical School, UTHealth, and the greater Texas Medical Center. Fluorescence microscopy and image analysis core. | ABRF, Fluorescence microscopy, image analysis, advanced light microscopy techniques, quantitative image analysis, |
is listed by: ABRF CoreMarketplace has parent organization: University of Texas Health Science Center at Houston; Texas; USA |
Restricted | ABRF_2967 | https://coremarketplace.org/?FacilityID=2967&citation=1 | SCR_025962 | Center for Advanced Microscopy at UTHealth at Houston, , McGovern Medical School Center for Advanced Microscopy | 2026-08-14 09:29:09 | 10 | |||||||
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Emory University Pediatric Biostatistics Core Facility Resource Report Resource Website 1+ mentions |
Emory University Pediatric Biostatistics Core Facility (RRID:SCR_025834) | service resource, access service resource, core facility | Offers statistical expertise and services. Provides assistance and collaboration in study design, grant applications, protocol development, data analysis, publication preparation, and statistical education. | ABRF, statistical expertise, services, study design, grant applications, protocol development, data analysis, publication preparation, statistical education, |
is listed by: ABRF CoreMarketplace has parent organization: Emory University; Georgia; USA |
Restricted | ABRF_2924 | https://coremarketplace.org/?FacilityID=2924&citation=1 | SCR_025834 | , Emory University and Children's Healthcare of Atlanta Pediatric Biostatistics Core, EU-Pediatric Biostatistics Core, Emory University EU-Pediatric Biostatistics Core | 2026-08-14 09:29:19 | 9 | |||||||
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Harvard Medical School Single Cell Core Facility Resource Report Resource Website 1+ mentions |
Harvard Medical School Single Cell Core Facility (RRID:SCR_025837) | SCC | service resource, access service resource, core facility | Core specializes in single cell and spatial transcriptomics, and multiomics. Provides custom services, education, training and expertise in multiple high-throughput single cell technologies. | single cell, spatial transcriptomics, multiomics, single cell technologies, |
is listed by: ABRF CoreMarketplace has parent organization: Harvard Medical School; Massachusetts; USA |
Open | ABRF_2939 | https://coremarketplace.org/?FacilityID=2939&citation=1 | SCR_025837 | Harvard Medical School Single Cell Core, Single Cell Core | 2026-08-14 09:29:20 | 5 | ||||||
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BWA-METH Resource Report Resource Website 10+ mentions |
BWA-METH (RRID:SCR_025851) | image analysis software, data processing software, software application, software resource, source code, alignment software | Software tool for fast and accurate alignment of BS-Seq reads using bwa-mem and 3-letter genome. | alignment of BS-Seq reads, alignment, BS-Seq reads, bwa-mem, 3-letter genome, | Free, Available for download, Freely available | SCR_025851 | bwa-meth | 2026-08-14 09:29:44 | 28 | ||||||||||
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University of California at Berkeley Vincent J. Coates Proteomics/Mass Spectrometry Laboratory Core Facility Resource Report Resource Website 10+ mentions |
University of California at Berkeley Vincent J. Coates Proteomics/Mass Spectrometry Laboratory Core Facility (RRID:SCR_025852) | service resource, access service resource, core facility | Core provides multidimensional LC-MS/MS analysis including Protein ID, Proteomics Profiling, Targeted Proteomics and Post Translational Modification analysis. Quantitative proteomic services are provided using label free quantitative proteomic (LFQ) profiling, Tandem mass tagging (TMT) or SILAC approaches. Provides support for macromolecular complexes using Nano ESI. | multidimensional LC-MS/MS analysis, Protein ID, Proteomics Profiling, Targeted Proteomics, Post Translational Modification, |
is listed by: ABRF CoreMarketplace has parent organization: University of California at Berkeley; Berkeley; USA |
ABRF_2944 | https://coremarketplace.org/?FacilityID=2944&citation=1 | SCR_025852 | UCB Proteomics/Mass Spectrometry Laboratory | 2026-08-14 09:29:20 | 13 | ||||||||
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PHP Resource Report Resource Website 10+ mentions |
PHP (RRID:SCR_025974) | programming language, software resource | Popular general-purpose scripting language that is especially suited to web development. | scripting language, web development, | Free, Freely available | SCR_025974 | Hypertext Preprocessor | 2026-08-14 09:29:44 | 29 | ||||||||||
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expanded Human Oral Microbiome Database Resource Report Resource Website 50+ mentions |
expanded Human Oral Microbiome Database (RRID:SCR_025964) | eHOMD | database, data or information resource | Provides comprehensive curated information on bacteria in human mouth and aerodigestive tract, including pharynx, nasal passages, sinuses and esophagus. eHOMD taxonomy provides provisional naming scheme for currently unnamed taxa, based on 16S rRNA sequence phylogeny, so that strain, clone and probe data from any laboratory can be directly linked to a stably named reference scheme. | curated information, bacteria in human mouth and aerodigestive tract, bacteria, human mouth, aerodigestive tract, pharynx, nasal passages, sinuses, esophagus, | NIDCR RO1 DE016937 | Free, Freely available, | SCR_025964 | 2026-08-14 09:29:20 | 70 | |||||||||
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Harvard Medical School Nascent Transcriptomics Core Facility Resource Report Resource Website 1+ mentions |
Harvard Medical School Nascent Transcriptomics Core Facility (RRID:SCR_025844) | service resource, access service resource, core facility | Core specializes in analysis of nascent transcriptome using PRO-seq and TT-seq NGS methods. Provides services allowing users to submit prepared cells and receive analyzed data. Offers free consultations to help with experimental design, answer questions, and discuss data analysis. | analysis of nascent transcriptome, PRO-seq, TT-seq, NGS methods, |
is listed by: ABRF CoreMarketplace has parent organization: Harvard Medical School; Massachusetts; USA |
ABRF_2940 | https://coremarketplace.org/?FacilityID=2940&citation=1 | SCR_025844 | Nascent Transcriptomics Core, Harvard Medical School Nascent Transcriptomics Core | 2026-08-14 09:29:44 | 1 | ||||||||
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ggpicrust2 Resource Report Resource Website 10+ mentions |
ggpicrust2 (RRID:SCR_025965) | software toolkit, source code, software resource | Software R package for analyzing and interpreting results of PICRUSt2 functional prediction. Offers range of features, including pathway name/description annotations, advanced differential abundance methods, and visualization of differential abundance results. Used for PICRUSt2 predicted functional profile analysis and visualization. | PICRUSt2 predicted functional profile analysis and visualization, analyzing and interpreting results of PICRUSt2, PICRUSt2 functional prediction, differential abundance visualization, | NIA 5P30AG072959; NIDDK 3R01DK042191 |
PMID:37527009 | Free, Available for download, Freely available | SCR_025965 | 2026-08-14 09:29:09 | 17 | |||||||||
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LinDA Resource Report Resource Website 1+ mentions |
LinDA (RRID:SCR_025966) | data processing software, software application, data analysis software, software resource, source code | Software linear models for differential abundance analysis of microbiome compositional data. Used to tackle compositional effects in differential abundance analysis. It fits linear regression models on centered log2-ratio transformed data, identifies bias term due to transformation and compositional effect, and corrects bias using mode of regression coefficients. It could fit mixed-effect models. | differential abundance analysis, microbiome compositional data, differential abundance analysis, | NIGMS R01GM144351; NSF ; Mayo Clinic Center for Individualized Medicine |
PMID:35421994 | SCR_025966 | Linear models for differential abundance analysis of microbiome compositional data (LinDA), Linear models for differential abundance analysis of microbiome compositional data | 2026-08-14 09:29:44 | 4 | |||||||||
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Selenium WebDriver Resource Report Resource Website 1+ mentions |
Selenium WebDriver (RRID:SCR_025969) | source code, software application, software resource | Software remote control interface that enables introspection and control of user agents. Provides platform- and language-neutral wire protocol as way for out-of-process programs to remotely instruct behavior of web browsers. | Remote control interface, introspection and control of user agents, platform- and language-neutral wire protocol, remotely instruct behavior of web browsers, | Free, Available for download, Freely available | https://github.com/w3c/webdriver | SCR_025969 | WebDriver | 2026-08-14 09:29:09 | 2 | |||||||||
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PRROC Resource Report Resource Website 10+ mentions |
PRROC (RRID:SCR_026113) | software toolkit, source code, software resource | Software package for computing and visualizing precision-recall and receiver operating characteristic curves in R for weighted and unweighted data. | Computing and visualizing precision-recall, receiver operating characteristic curves, weighted and unweighted data, | PMID:25810428 | Free, Available for download, Freely available | SCR_026113 | Precision-Recall and Receiver Operating Characteristic | 2026-08-14 09:29:11 | 10 | |||||||||
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data.table Resource Report Resource Website 10+ mentions |
data.table (RRID:SCR_026117) | software toolkit, source code, software resource | Software R data.table package extends data.frame. Provides high-performance version of base R's data.frame with syntax and feature enhancements for ease of use, convenience and programming speed. | extends data.frame, syntax and feature enhancements, syntax, feature, enhancements | Free, Available for download, Freely available | SCR_026117 | 2026-08-14 09:29:11 | 13 | |||||||||||
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Dartmouth Geisel School of Medicine Biological Mass Spectrometry and Proteomics Shared Resource Core Facility Resource Report Resource Website 1+ mentions |
Dartmouth Geisel School of Medicine Biological Mass Spectrometry and Proteomics Shared Resource Core Facility (RRID:SCR_026076) | service resource, access service resource, core facility | Core offers quantitative and qualitative proteomics services using LC-MS/MS technologies. Servies include sample preparation from harvested cell pellets, elutions post-enrichment or purification, or gel bands through data acquisition, quantification, and statistical analysis. | ABRF | ABRF_2974 | https://coremarketplace.org/?FacilityID=2974&citation=1 | SCR_026076 | , Biological Mass Spectrometry and Proteomics, Geisel School of Medicine at Dartmouth Biological Mass Spectrometry and Proteomics | 2026-08-14 09:29:22 | 2 | |||||||||
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VirtualDub Resource Report Resource Website 10+ mentions |
VirtualDub (RRID:SCR_026123) | software application, software resource | Open-source software for video capture and video processing for Microsoft Windows. Designed to process linear video streams, including filtering and recompression. It uses AVI container format to store captured video. Video capture/processing utility for 32-bit and 64-bit Windows platforms. Used for processing AVI files, although it can read (not write) MPEG-1 and also handle sets of BMP images. | video capture, video processing, process linear video streams, filtering, recompression, processing AVI files, | Free, Available for download, Freely available | https://sourceforge.net/projects/virtualdub/files/ | SCR_026123 | 2026-08-14 09:29:11 | 19 | ||||||||||
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R plus Resource Report Resource Website 1+ mentions |
R plus (RRID:SCR_026005) | source code, algorithm resource, software resource | Software provides direct mapping refence between expanded molecular alphabet and N-nary digits in the absence of high-performance transcoding algorithm at present. Transcoding scheme for DNA data storage based on expanded molecular alphabet. | Transcoding scheme, DNA data storage, expanded molecular alphabet, DNA, storage, | Free, Available for download, Freely available | SCR_026005 | 2026-08-14 09:29:21 | 1 | |||||||||||
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HVSeeker Resource Report Resource Website 1+ mentions |
HVSeeker (RRID:SCR_026120) | software application, software resource | Software tool for distinguishing between bacterial and phage sequences. Consists of two separate models: one analyzing DNA sequences and the other focusing on proteins. | genome, bacteria, phage, sequence, distinguishing between bacterial and phage sequences, | German Research Foundation INST 37/935-1 FUGG; King Fahd University of Petroleum and Minerals |
Free, Available for download, Freely available, | SCR_026120 | 2026-08-14 09:29:11 | 1 | ||||||||||
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DeepMEI Resource Report Resource Website 1+ mentions |
DeepMEI (RRID:SCR_026119) | data processing software, software application, data analysis software, source code, software resource | Software tool to detect mobile element insertion in human short read sequencing data. | detect mobile element insertion, human short read sequencing data, | Free, Available for download, Freely available | SCR_026119 | 2026-08-14 09:29:22 | 1 | |||||||||||
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Basement Membrane Extract (BME)-free Database Resource Report Resource Website 1+ mentions |
Basement Membrane Extract (BME)-free Database (RRID:SCR_026058) | database, data or information resource | Database with products that can serve as alternative for basement membrane extracts (BMEs) for in vitro applications. BME-free database is publicly available and is part of 3Rs Research Tools Programme, which is managed and hosted by 3Rs Centre Utrecht. | BME-free database, alternative for basement membrane extracts, 3Rs Centre Utrecht, | has parent organization: Utrecht University; Utrecht; Netherlands | Restricted | SCR_026058 | 2026-08-14 09:29:45 | 1 |
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