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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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Biomedicum Genomics Resource Report Resource Website |
Biomedicum Genomics (RRID:SCR_003907) | BMGen | commercial organization | Organization that provides academic and industrial clients access to functional genomics technologies, services and partnering solutions including genome-wide expression, copy number profiling, miRNA expression, DNA-protein interaction (ChIP-on-chip), Illumina high-throughput sequencing including nucleic acid quality and quantity assessment. For gene silencing and ectopic expression purposes, they offer high-titer shRNA and ORF lentiviruses targeting genes of interest. They also offer customized services e.g. preparation of gain or loss-of-function cell lines and protein interactomics-based services (yeast two-hybrid). In addition, they provide access to wide array of computational data analyses. BMGen also offers partnering deals for clients interested in customized integration of several technologies. | genomics, functional genomics, genome-wide expression, copy number profiling, mirna expression, dna-protein interaction, chip-on-chip, illumina, high-throughput sequencing, nucleic acid, quality assessment, quantity assessment, data analysis | is related to: PREDECT | nlx_158263 | http://www.bmgen.fi | SCR_003907 | Biomedicum Genomics Ltd, Biomedicum Genomics Oy | 2025-04-19 06:41:57 | 0 | |||||||
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Quartz Bio Resource Report Resource Website |
Quartz Bio (RRID:SCR_003919) | QBIO | commercial organization | A Swiss service and consulting company specialized in the computational analysis of biomarker data from clinical trials. Their technical expertise spans across multiple biomaker technological platforms such as genetics, transcriptomics, protein assays and cellular assays. Quartz Bio is a spin-off of Merck Serono with the capital of the company entirely owned by its employees. | clinical, bioinformatics, medicine, biomarker, clinical trial, data analysis | is related to: PRECISESADS | nlx_158280 | SCR_003919 | Quartz Bio S.A. | 2025-04-19 06:41:58 | 0 | ||||||||
|
EDASeq Resource Report Resource Website 100+ mentions |
EDASeq (RRID:SCR_006751) | EDASeq | software resource | Software for numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010). | data analysis, normalization, rna-seq |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: National Cancer Institute |
OMICS_01231 | SCR_006751 | EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq data | 2025-04-19 06:43:46 | 237 | ||||||||
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Agilent 2100 Bioanalyzer Instrument Resource Report Resource Website 100+ mentions |
Agilent 2100 Bioanalyzer Instrument (RRID:SCR_018043) | instrument resource | Bioanalyzer system is automated electrophoresis tool that providesa analytical evaluation of various samples types in many workflows, including next generation sequencing NGS, gene expression, biopharmaceutical, and gene editing research. Digital data is provided in timely manner and delivers assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for accurate result, and data may be exported in many different formats. | ABRF, bioanalyzer, electrophoresis, DNA, RNA, protein, data analysis, instrument, equipment | is listed by: USEDit | SCR_019389, Model_Number_2100 Bioanalyzer | https://www.agilent.com/cs/library/usermanuals/public/2100_Bioanalyzer_Expert_USR.pdf | SCR_018043 | Agilent 2100 Bioanalyzer, , 2100 Bioanalyzer (Agilent Technologies) | 2025-04-21 11:00:42 | 144 | ||||||||
|
CaspBase Resource Report Resource Website 1+ mentions |
CaspBase (RRID:SCR_018975) | data or information resource, database | Database for evolutionary biochemical studies of caspase functional divergence and ancestral sequence inference. Tool to rapidly disseminate organized caspase sequence data. Includes all animal species with currently available annotated genomes in NCBI genome database. Manually curated and not curated sequences are available to download. | Caspase sequences, curated data, caspase, caspase functional divergence, ancestral sequence inference, data analysis, dataset |
is related to: NCBI Genome is related to: NCBI |
PMID:30076665 | Free, Available for download, Freely available | SCR_018975 | Caspase Sequence Database | 2025-05-06 11:14:10 | 2 | ||||||||
|
Wistar Bioinformatics Core Facility Resource Report Resource Website |
Wistar Bioinformatics Core Facility (RRID:SCR_010203) | BCF, WI, WI BCF | core facility, service resource, access service resource | Core provides High Throughput Data Analysis, Customized Bioinformatics Services, Custom Programming, High Performance Computing, Data management. Located in the Center for Systems and Computational Biology. Provides Cancer Center investigators with database management, software application support, expertise in statistical analyses and computational modeling of biomedical research data. | Bioinformatics Facility, Wistar, mass spectrometry, data analysis, genotyping, protein expression profiling, rna, sequencing, chip-chip, assay, bioinformatics analysis, non-web programming, database development, grid computing, data, Jmanagement, storage |
is listed by: Eagle I is listed by: ABRF CoreMarketplace has parent organization: Wistar Institute |
Open | ABRF_2803, nlx_156682 | https://coremarketplace.org/?FacilityID=2803&citation=1 | https://wistar.org/our-science/shared-facilities/bioinformatics-facility, http://eagle-i.itmat.upenn.edu/i/00000138-7c98-bfbf-fbab-3b8480000000 | SCR_010203 | Bioinformatics Core, Bioinformatics Core Facility | 2025-05-07 11:53:10 | 0 | |||||
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Sanford-Burnham Applied Bioinformatics Core Facility Resource Report Resource Website |
Sanford-Burnham Applied Bioinformatics Core Facility (RRID:SCR_012208) | Sanford-Burnham Applied Bioinformatics Core | core facility, service resource, access service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented January 23, 2019. Core supports SBMRI investigators in exploring, understanding and analyzing complex biological data. Core is equipped with cutting-edge computational infrastructure and a selective collection of bioinformatics software. Core's services include consultation, data analysis and management, software development, and accessing to large computing resources. To meet various demands from the investigators, we provide services at multiple levels, from full service to cost-effective limited service as well as collaborative projects requiring longer-term commitment of time and effort. | data analysis, infrastructure, |
is listed by: ScienceExchange has parent organization: Sanford Burnham Prebys Medical Discovery Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_10624 | SCR_012208 | , Applied Bioinformatics Core, Sanford-Burnham, Medical Research Institute | 2025-05-07 11:54:10 | 0 | |||||||
|
La Jolla Institute for Allergy and Immunology Bioinformatics Core Facility Resource Report Resource Website |
La Jolla Institute for Allergy and Immunology Bioinformatics Core Facility (RRID:SCR_014831) | core facility, service resource, access service resource | Core Facility provides support for short or long-term projects requiring expertise the analysis of biological datasets. The services provided include the analysis of large-scale datasets (e.g. next-gen sequencing data, microarrays, etc.), the development of customized databases and reusable analysis pipelines, guidance on experimental design, support with technical sections of manuscripts and grants, and training on analysis software packages. All services are charged at our hourly rate. | immunology, core facility, la jolla, bioinformatics, core facility, data analysis, pipeline development, technical, statistical, review, training |
has parent organization: La Jolla Institute for Allergy and Immunology has organization facet: Immune Epitope Database and Analysis Resource (IEDB) |
Available to external user | http://livesite.liai.org/pages/core_bioinformatics | SCR_014831 | Institute for Immunology, La Jolla Institute; La Jolla Institute for Allergy and Immunology Bioinformatics Core; | 2025-05-07 11:55:52 | 0 | ||||||||
|
Flowing Software 2.5.1 Resource Report Resource Website 100+ mentions |
Flowing Software 2.5.1 (RRID:SCR_015781) | data analysis software, data processing software, software application, software resource | Software for flow cytometry data analysis. Flowing Software has many common analysis tools, such as dot plots, histograms, quadrants, statistics, overlay histograms etc. | cytometry, flow cytometry, flow cytometry data, data analysis, box plot, histogram, quadrant, statistic, overlay histogram | Free, Available for download | http://www.flowingsoftware.com/ https://en.freedownloadmanager.org/users-choice/Flowing_Software_2.5.1.html |
SCR_015781 | Flowing Software | 2025-05-12 11:17:10 | 111 | |||||||||
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Neural Decoding Toolbox Resource Report Resource Website 10+ mentions |
Neural Decoding Toolbox (RRID:SCR_009012) | NDT | data processing software, software application, software toolkit, software resource, data analysis software | Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations. | population decoding, neuron, analysis, matlab, data analysis, machine learning, multivariate pattern analysis, neural decoding | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | DARPA ; IPTO ; DSO ; AFSOR-THRL ; Adobe Systems ; Honda Research Institute USA ; King Abdullah University of Science and Technology ; NEU ; Sony ; Eugene McDermott Foundation ; NSF 0640097; NSF 0827427; NSF FA8650-05-C-7262 |
PMID:23734125 | Acknowledgement requested, Account required | nlx_152729 | SCR_009012 | 2025-05-12 11:10:34 | 16 | ||||||
|
Consortium for Functional Glycomics (CFG) Resource Report Resource Website 1+ mentions |
Consortium for Functional Glycomics (CFG) (RRID:SCR_013689) | CFG | portal, data or information resource, organization portal, consortium | The Consortium for Functional Glycomics (CFG) serves to combine the expertise and glycomics resources to reveal functions of glycans and glycan-binding proteins (GBPs) that impact human health and disease. The CFG offers resources to the community free of charge, including glycan array screening services, a reagent bank, and access to a large glycomics database and data analysis tools. | glycomics, glycans, screening, reagent bank, reagent, database, data analysis, | Glyncominds Ltd. ; Kyowa Hakko Kogyo Co Ltd. ; Momenta Pharmaceuticals ; National Center for Research Resources ; National Institute for General Medicine Sciences ; National Research Council Canada ; Neose Technologies Inc. ; Otsuka Chemical Holdings Co. Ltd |
SCR_013689 | 2025-05-12 11:15:03 | 4 | ||||||||||
|
StatCrunch Resource Report Resource Website 10+ mentions |
StatCrunch (RRID:SCR_013992) | software resource, data or information resource, web application | A web application which allows users to collect data, perform complex analyses, and generate results. Users can upload data sets from their computer or from the internet for data analysis and graph creation which can be saved, printed, and downloaded. More than 15,000 statistical data sets are available. | web application, statistics, data analysis, data set, graph |
is listed by: Connected Researchers is related to: Connected Researchers |
The community can contribute to this resource | SCR_013992 | 2025-05-12 11:15:15 | 10 | ||||||||||
|
Wakari Resource Report Resource Website 1+ mentions |
Wakari (RRID:SCR_013995) | software resource, web application | A web application which performs Python data analysis. Users can create IPython notebooks to hold uploaded data and use various tools to describe, analyze, and visualize the data. Notebooks, data, and Anaconda environments can be shared as "bundles" with other users, who can edit and download them. | web application, data analysis, Python data analysis, visualization |
uses: IPython Notebook is listed by: Connected Researchers is related to: Connected Researchers is related to: IPython Notebook |
Free, Fee (for different packages) | SCR_013995 | 2025-05-12 11:15:15 | 1 | ||||||||||
|
APERTURE Resource Report Resource Website 1+ mentions |
APERTURE (RRID:SCR_014082) | data processing software, software application, software toolkit, software resource, data analysis software, workflow software | A MATLAB-based toolbox for analysis of EEG, MEG, and ECoG data. APERTURE allows flexible multivariate analysis of ERPs and oscillatory activity and supports mass-univariate analysis with advanced statistical tests. Computations are accelerated using parallel computing supported through the MATLAB distributed computing toolbox. Examination of large, high-dimensional datasets is made simple through data visualization tools, including advanced plotting routines and generation of PDF reports with many figures. | matlab, software toolkit, workflow software, toolbox, multivariate analysis, data analysis |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Vanderbilt University; Tennessee; USA |
SCR_014082 | Analysis of Patterns in Electrophysiological Recordings Toolbox with Utilities for REsearch | 2025-05-12 11:15:19 | 3 | ||||||||||
|
SnpHub Resource Report Resource Website 1+ mentions |
SnpHub (RRID:SCR_018177) | software resource, web application | Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. | Genomic, data, data visualization, data analysis, data retrieving, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31701415; National Key Research and Development Program of China 2018YFD0100803; National Key Research and Development Program of China 2016YFD0100801 |
Free, Available for download, Freely available | biotools:SnpHub | http://guoweilong.github.io/SnpHub/ https://bio.tools/SnpHub |
SCR_018177 | 2025-05-12 11:19:41 | 1 | |||||||
|
Data-Against-COVID Team Resource Report Resource Website |
Data-Against-COVID Team (RRID:SCR_018288) | topical portal, portal, data or information resource | Group of volunteer data scientists, machines learning experts, bioinformaticians and professional software developers who have joined together to offer their expertise for any data analysis problems that arise in context of ongoing coronavirus pandemic. | Data scientist, volunteer, machine learning expert, bioinformaticians, professional software developer, data analysis, coronavirus pandemic | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | Free, Freely available | SCR_018288 | 2025-05-12 11:19:47 | 0 | |||||||||
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Biolucida Resource Report Resource Website 1+ mentions |
Biolucida (RRID:SCR_018256) | data processing software, data management software, software resource, software application, data analysis software, data storage software | Enables visualization, storage and sharing of large image data. Cloud based system by MBF Bioscience to help with data from 2D and 3D slide scanners, confocal Z-stacks, lightsheet whole brain images. System for data storage and management, data analysis and visualization. Data is stored in secure and permanent way. Available also is free application named Biolucida Viewer, for viewing public images or images shared by collaborators owning Biolucida. | biolucida, big data, image, Microscopy, whole slide images, virtual images, cloud, visualization, data storage, data analysis | is used by: SPARC Project | DOI:10.1002/cne.23329 | Restricted | http://wiley.biolucida.net/link/ | SCR_018256 | , Micro File Plus, MicroFile+, MicroFile | 2025-05-12 11:19:45 | 5 | |||||||
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R scripts for FLIC data analysis Resource Report Resource Website 1+ mentions |
R scripts for FLIC data analysis (RRID:SCR_018386) | data processing software, source code, software application, software resource, data analysis software | R Code used to analyze FLIC data. Functions are provided to examine interactions with food for single well and food choice experiments when fly makes physical contact with liquid food. | Fly Liquid Food Interaction Counter, FLIC, FLIC data analysis, fly physical contact, liquid food fly interaction, data analysis | PMID:24978054 | Free, Available for download, Freely available | https://github.com/PletcherLab/FLIC_R_Code | SCR_018386 | R scripts for Fly Liquid Food Interaction Counter data analysis | 2025-05-12 11:19:53 | 7 | ||||||||
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Monocle3 Resource Report Resource Website 100+ mentions |
Monocle3 (RRID:SCR_018685) | data processing software, software application, software toolkit, software resource, data analysis software | Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. | Data analysis, singel cell RNAseq data, single cell RNAseq experiment, transcriptome dynamics | has parent organization: University of Washington; Seattle; USA | NIH Office of the Director DP2 OD00667; NIGMS P01 GM099117; NIH Office of the Director DP2 0D008514; NHGRI P50 HG006193; Single Cell Genomics initiative |
PMID:24658644 | Free, Available for download, Freely available | https://github.com/cole-trapnell-lab/monocle3 | SCR_018685 | Monocle, Monocle 3 | 2025-05-12 11:20:09 | 205 | ||||||
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DAMBE Resource Report Resource Website 1+ mentions |
DAMBE (RRID:SCR_018528) | data processing software, software application, software resource, sequence analysis software, data analysis software | Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. | Data analysis, molecular sequence data, genomic data, phylogenetic data, data, anaysis, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Ottawa; Ontario; Canada |
Natural Science and Engineering Research Council of Canada ; University of Hong Kong ; Hong Kong Research Grant Council |
PMID:11535656 PMID:28379490 PMID:23564938 PMID:29669107 |
Free, Available for download, Freely available | biotools:dampe | https://bio.tools/dambe | SCR_018528 | DAMBE6, DAMBE5, DAMBE7, Data Analysis in Molecular Biology and Evolution | 2025-05-12 11:20:00 | 5 |
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