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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.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Authority Synonyms Record Last Update Mentions Count
rlsim
 
Resource Report
Resource Website
rlsim (RRID:SCR_001703) rlsim software resource Software package for simulating RNA-seq library preparation with parameter estimation. rna-seq is listed by: OMICtools
has parent organization: European Bioinformatics Institute
Free, Available for download, Freely available OMICS_01965 SCR_001703 SciCrunch Registry rlsim - a package for simulating RNA-seq library preparation with parameter estimation 2026-10-17 01:24:58 0
PoissonSeq
 
Resource Report
Resource Website
10+ mentions
PoissonSeq (RRID:SCR_001784) PoissonSeq software resource Software package that implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data. normalization, testing, false discovery rate, rna-seq is listed by: OMICtools
has parent organization: Stanford University; Stanford; California
PMID:22003245 Free, Available for download, Freely available OMICS_01950 http://cran.r-project.org/web/packages/PoissonSeq/index.html SCR_001784 SciCrunch Registry PoissonSeq: Significance analysis of sequencing data based on a Poisson log linear model 2026-10-17 01:25:22 34
Mount Sinai School of Medicine: In-Vivo Molecular Imaging Laboratory
 
Resource Report
Resource Website
Mount Sinai School of Medicine: In-Vivo Molecular Imaging Laboratory (RRID:SCR_001785) analysis service resource, biomaterial analysis service, data computation service, material analysis service, production service resource, service resource The In-Vivo Molecular Imaging Laboratory (IMIL) is a MSSM shared resource facility serving the research community of Mount Sinai with equipment and imaging expertise. State-of-the-art bioluminescent as well as fluorescent imaging modalities are supported for in-vivo monitoring of cellular and genetic activity. Investigators are provided with cutting edge imaging technologies as well as analysis techniques. The long-term goal is to establish a comprehensive SRF for in-vivo molecular imaging using micro-MRI, micro-PET and other modalities. IMIL houses a Xenogen IVIS-200 Series imaging system with the integrated fluorescent imaging options. Simultaneous dual reporter in-vivo imaging is possible with bioluminescence and fluorescence probes. The imaging chamber has a gas anesthesia manifold that can accommodate up to 5 mice for simultaneously image acquisition. Selectable field of views allow in-plane (X,Y) imaging resolutions of up to 60-microm. Integrated spectra filters allow for the determination of signal source depth (Z). IMIL will provide data acquisition services as well as analysis. IMIL has a dedicated imaging technologist for data acquisition. Investigators will bring their prepared animal to the lab and an IMIL imaging technologist will assist in sedating the animals and acquire imaging data. Typical imaging sessions last about an hour. Certified users who are trained in the use of the software will be able to perform their own analysis at the console. Usage of the imaging device is charged by the hour ($100/hour). Structural Imaging The IVIS-200 has the built-in capability of obtaining an image of the surface topography of the animal for 2D and 3D localization. If additional true 3D imaging data is required, micro MRI is available through the Imaging Science Laboratories (ISL). Image Analysis The IVIS-200 has an integrated image acquisition and analysis software (Living Image Software 2.50). Comprehensive data quantification is possible with this software. Raw data as well as analyzed results can be electronically transferred to the investigators. Support is also available for additional image analysis such as intermodality coregistration, 3D rendering, and group statistics. Additional software packages include MedX, SPM, Brainvoyager, Analyze, and in-house developed software. equipment, fluorescence, fluorescent, genetic, 2d, 3d, analysis, bioluminescence, bioluminescent, cellular, imaging, intermodality coregistration, in-vivo, localization, mice, micro-mri, micro-pet, molecular, probe, software, spectra, technology, xenogen ivis-200 series has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA Free, Freely available nif-0000-10299 http://www.mssm.edu/research/resources/molecular_imaging/ SCR_001785 SciCrunch Registry MSSM IMIL 2026-10-17 01:25:00 0
MEME Suite - Motif-based sequence analysis tools
 
Resource Report
Resource Website
1000+ mentions
MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) MEME Suite analysis service resource, data analysis service, data analysis software, data or information resource, data processing software, database, production service resource, service resource, software application, software resource, source code Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use. gene ontology, motif, comparative genomics, dna regulatory motif, dna sequence, dna, gene, transcription factor, genome, protein, analysis, function analysis, comparison, cluster, enrichment analysis, sequence analysis, bio.tools, FASEB list lists: DREME
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
is related to: Glam2
is related to: ANNOgesic
is related to: memesuite-lite
has parent organization: National Biomedical Computation Resource
is parent organization of: GOMO - Gene Ontology for Motifs
NCRR R01 RR021692 PMID:19458158
DOI:10.1093/nar/gkl198
Free, Freely available nif-0000-10298, biotools:meme_suite, OMICS_08103 https://bio.tools/meme_suite http://meme.sdsc.edu/meme4_6_1/intro.html, http://meme.nbcr.net/meme/, https://sources.debian.org/src/meme/ SCR_001783 SciCrunch Registry The MEME Suite 2026-10-17 01:25:08 2472
Sample of Science
 
Resource Report
Resource Website
Sample of Science (RRID:SCR_001656) Sample of Science access service resource, data or information resource, database, journal article, service resource THIS RESOURCE IS NO LONGER IN SERVICE.

Free access service resource dedicated to connect researchers creating scientific samples with scientists who need samples for their experiments. With Sample of Science researchers can submit samples, or contact scientists proposing sample for dissemination. Each disseminated sample also gets its description published in Sample of Science Bulletin, a dedicated open access journal. It acquires a Digital Object Identifier (DOI) and becomes a fully citable item. Because both adequate sample descriptions and mutually-agreed dissemination conditions are key factors for a fruitful dissemination that respects mutual interest, Sample of Science provides tools to elaborate, communicate, discuss, and refine both sample description and dissemination conditions. This process, termed peer-adoption process, results in the publication of disseminated sample descriptions in Sample of Science Bulletin, a dedicated open access publication. The publication in Sample of Science Bulletin is useful to provide adequate recognition to Sample Authors who contribute to the development of science by offering visibility to their disseminated samples. To the adopter it provides experimental details regarding the sample under the form of a citable reference useful for any future publications involving this sample. To a larger scientific community interested in material science, it provides a useful tool to stay abreast the activity of sample providers in their respective field of expertise.
nanorod, nanoprobe, imaging, biomedical, fluorescence, nanostructure, graphene, nanomaterial, magnetic material, metal-organic framework, community building portal THIS RESOURCE IS NO LONGER IN SERVICE nlx_153937 https://www.sampleofscience.net/ SCR_001656 SciCrunch Registry 2026-10-17 01:24:58 0
RSVSim
 
Resource Report
Resource Website
10+ mentions
RSVSim (RRID:SCR_001777) software resource A software package for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates. unix/linux, mac os x, windows, r, sequencing, structural variation is listed by: OMICtools
has parent organization: Bioconductor
PMID:23620362 Free, Available for download, Freely available OMICS_03822 SCR_001777 SciCrunch Registry RSVSim: an R/Bioconductor package for the simulation of structural variations 2026-10-17 01:25:22 16
Annual Reviews: A Nonprofit Scientific Publisher
 
Resource Report
Resource Website
10+ mentions
Annual Reviews: A Nonprofit Scientific Publisher (RRID:SCR_001655) journal article Annual Reviews offers comprehensive, timely collections of critical reviews written by leading scientists. It publishes authoritative, analytic reviews in 37 focused disciplines within the Biomedical, Life, Physical, and Social Sciences. The mission of Annual Reviews is to provide systematic, periodic examinations of scholarly advances in a number of fields of science through critical authoritative reviews. The comprehensive critical review not only summarizes a topic but also roots out errors of fact or concept and provokes discussion that will lead to new research activity. The critical review is an essential part of the scientific method. Sponsors: Annual Reviews is a non-profit organization created and managed by scientists to serve science by publishing reviews in 40 different scientific fields. biomedical, life science, literature, physical science, review, social science Free, Freely Available nif-0000-10150 SCR_001655 SciCrunch Registry Annual Reviews 2026-10-17 01:25:17 31
TCC
 
Resource Report
Resource Website
10+ mentions
TCC (RRID:SCR_001779) TCC software resource An R package that provides a series of functions for differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in other sophisticated packages (especially edgeR, DESeq, and baySeq). rna-seq, differential expression, high throughput sequencing is listed by: OMICtools
has parent organization: Bioconductor
has parent organization: University of Tokyo; Tokyo; Japan
PMID:23837715 Free, Available for download, Freely available OMICS_01952 SCR_001779 SciCrunch Registry Tag Count Comparison, TCC: Differential expression analysis for tag count data with robust normalization strategies 2026-10-17 01:25:00 10
Salk Institute for Biological Studies - Slesinger Lab
 
Resource Report
Resource Website
Salk Institute for Biological Studies - Slesinger Lab (RRID:SCR_001850) data or information resource, portal, topical portal THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This lab is investigating the molecular details of how potassium ion channels open and close (i.e. gating), the cellular regulation of potassium channels in nerve cells, and more recently, their role in drug addiction and mental disorders. There are currently two related areas of focus in the lab. One main area of research is investigating the G protein regulation of GIRK channels, utilizing structural, biochemical and electrophysiological strategies. The other area extends from the G protein regulation experiments to studies that examine the role of GIRK channels in the neural response to drugs of abuse, utilizing biochemical, electrophysiological and behavioral strategies. drug, electrophysiological, gating, abuse, addiction, behavioral, biochemical, cell, cellular, channel, disorder, girk channel, g protein, ion, mental, molecular, nerve, neural, potassium, regulation, structural THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10413 SCR_001850 SciCrunch Registry Salk Institute (Slesinger) 2026-10-17 01:25:09 0
CCAT
 
Resource Report
Resource Website
50+ mentions
CCAT (RRID:SCR_001843) CCAT software resource THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Genome Institute of Singapore; Singapore; Singapore
PMID:20371496 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00428, biotools:ccat https://bio.tools/ccat SCR_001843 SciCrunch Registry Control based ChIP-Seq Analysis Tools 2026-10-17 01:25:01 76
GenABEL
 
Resource Report
Resource Website
500+ mentions
GenABEL (RRID:SCR_001842) software library, software resource, software toolkit THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits. r, genome-wide association, single nucleotide polymorphism is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: Debian
is listed by: SoftCite
Centre for Medical Systems Biology; Netherlands ;
Netherlands Genomics Initiative ;
Netherlands Organisation for Scientific Research ;
Russian Foundation for Basic Research
PMID:17384015
DOI:10.1186/1471-2105-11-134
DOI:10.1093/bioinformatics/btm108
THIS RESOURCE IS NO LONGER IN SERVICE nlx_154328, OMICS_00234 http://mga.bionet.nsc.ru/~yurii/ABEL/GenABEL/, https://cran.r-project.org/web/packages/GenABEL/index.html, https://sources.debian.org/src/probabel/ SCR_001842 SciCrunch Registry GenABEL package, R/GENABEL 2026-10-17 01:25:24 506
FreeSurfer
 
Resource Report
Resource Website
10000+ mentions
FreeSurfer (RRID:SCR_001847) FreeSurfer data processing software, data visualization software, image analysis software, software application, software resource Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS. processing, analysis, human, brain, MRI, image, reconstruction, cortical, surface, fMRI, data is used by: Wisconsin Cortical Thickness Analysis (CTA) Toolbox
is used by: freesurfR
is used by: Automatic Analysis
is used by: NHP Freesurfer
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
is listed by: Debian
is listed by: SoftCite
is related to: PySurfer
is related to: RFT FDR
is related to: FMRLAB
is related to: TRACULA
is related to: BASH4RfMRI
has parent organization: Harvard University; Cambridge; United States
has plug in: JOSA
works with: NIAG Addiction Data
NCRR RR014075;
NCRR U24 RR021382;
NINDS R01 NS052585
PMID:22248573 Free, Available for download, Freely available nif-0000-00304 https://sources.debian.org/src/freesurfer/, http://www.nitrc.org/projects/freesurfer, http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall SCR_001847 SciCrunch Registry 2026-10-17 01:25:25 12664
Alt Event Finder
 
Resource Report
Resource Website
Alt Event Finder (RRID:SCR_001846) Alt Event Finder software resource Software tool for deriving data-driven alternative splicing (AS) events from RNA-seq data. It analyses the transcripts built by Cufflinks or Scripture and outputs AS event annotations which is compatible with MISO. It can be used for annotating novel AS events from a well-annotated species such as human. It can also be used for species of which known AS event annotation is not available. The current release (v0.1) supports skipped exon events only. alternative splicing, rna-seq, alternative splicing event, transcript, annotation, splicing regulation is listed by: OMICtools
is related to: Cufflinks
is related to: Scripture
has parent organization: Indiana University; Indiana; USA
PMID:23281921 Free, Freely available OMICS_01941 SCR_001846 SciCrunch Registry Alt Event Finder: A tool for extracting alternative splicing events from RNA-seq data 2026-10-17 01:25:09 0
Stable Isotope Labeling with Amino Acids in Cell Culture
 
Resource Report
Resource Website
500+ mentions
Stable Isotope Labeling with Amino Acids in Cell Culture (RRID:SCR_001873) data or information resource, portal, topical portal Stable isotope labeling with amino acids in cell culture (SILAC) is a simple and straightforward approach for in vivo incorporation of a label into proteins for mass spectrometry (MS)-based quantitative proteomics. SILAC relies on metabolic incorporation of a given "light" or "heavy" form of the amino acid into the proteins. The method relies on the incorporation of amino acids with substituted stable isotopic nuclei (e.g. deuterium, 13C, 15N). In an experiment, two cell populations are grown in culture media that are identical except that one of them contains a "light" and the other a "heavy" form of a particular amino acid (e.g. 12C and 13C labeled L-lysine, respectively). When the labeled analog of an amino acid is supplied to cells in culture instead of the natural amino acid, it is incorporated into all newly synthesized proteins. After a number of cell divisions, each instance of this particular amino acid will be replaced by its isotope labeled analog. Since there is hardly any chemical difference between the labeled amino acid and the natural amino acid isotopes, the cells behave exactly like the control cell population grown in the presence of normal amino acid. It is efficient and reproducible as the incorporation of the isotope label is 100%. SILAC Applications: - Differential expression of proteins and identification of disease biomarkers - Cell signaling dynamics - Analysis of yeast pheromone signaling pathway - Identification of methylation sites - Identification of protease substrates - Study of protein complexes/protein interactions - Analysis of signaling pathways and effect of pharmacological inhibitors - Subcellular proteomics Sponsors: Supported in part by an NIH Roadmap grant Technology Center for Networks & Pathways of Lysine Modification. amino acid, analog, biomarker, cell culture, cell division, cell signal, chemical, deuterium, disease, inhibitor, in vivo, isotope, labeling, lysine, mass spectrometry, media, metabolic, methylation site, nucleus, pharmacological, protease, protein, protein complex, protein interaction, proteomics, signaling pathway, subcellular, substrate, yeast pheromone THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10435 SCR_001873 SciCrunch Registry SILAC 2026-10-17 01:25:02 673
ExpressionPlot
 
Resource Report
Resource Website
1+ mentions
ExpressionPlot (RRID:SCR_001904) expressionplot software resource Software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets. analysis, rna-seq, microarray, gene expression, affymetrix, prototype is listed by: OMICtools PMID:21797991 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01939 SCR_001904 SciCrunch Registry 2026-10-17 01:25:03 9
S-MART
 
Resource Report
Resource Website
10+ mentions
S-MART (RRID:SCR_001908) S-MART software resource Software toolbox that manages your RNA-Seq and ChIP-Seq data and also produces many different plots to visualize your data. It performs several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization. It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis. It also provides many ways to visualize data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots). A computer science background is not required to run it through a graphical interface and it can be run on any personal computer, yielding results within an hour for most queries. high throughput sequencing, rna-seq, chip-seq, python, linux, ms windows, mac, short-read, selection, visualization, bio.tools, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
PMID:21998740 Free, Available for download, Freely available OMICS_01937, biotools:mapperanalyzer, biotools:s-mart https://bio.tools/s-mart, https://bio.tools/mapperanalyzer SCR_001908 SciCrunch Registry 2026-10-17 01:25:03 24
Dendritica: Software Tools for Studying Dendritic Signaling
 
Resource Report
Resource Website
1+ mentions
Dendritica: Software Tools for Studying Dendritic Signaling (RRID:SCR_001865) simulation software, software application, software resource Dendritica is a program package for relating dendritic geometry and signal propagation. The programs are based on those used for the simulations described in the following paper: Vetter, P., Roth, A. & Husser, M. (2001). Action potential propagation in dendrites depends on dendritic morphology. Journal of Neurophysiology, 85: 926-937. Dendritica can functionally be divided into three main parts: - Interactive morphological analysis and electrophysiological simulation of single cells - Automated batch simulations across a set of morphologies using the same simulation parameters - Automated analysis of batch simulation runs Dendritica requires NEURON 4.1.1 with some modifications described in Appendix 1. It was tested for NEURON 4.1.1 on Linux and SGI IRIX. Some modifications to the Dendritica code may be necessary in order to run it on older or newer versions of NEURON. Sponsors: This work was supported by the Wellcome Trust, the European Community, the Max-Planck-Gesellschaft, the Wellcome Trust 4-year PhD Programme in Neuroscience. electrophysiological simulation, dendritic geometry, interactive, morphological, morphology, neuron, sigle cell, signal propagation Free http://www.dendrite.org/software.html SCR_001865 SciCrunch Registry Dendritica 2026-10-17 01:25:02 1
Stony Brook University Medical Center: Neuropathology Primer
 
Resource Report
Resource Website
Stony Brook University Medical Center: Neuropathology Primer (RRID:SCR_001866) book, data or information resource, narrative resource This is a primer of basic neuropathology- The Central Nervous System and Skeletal Muscle. It is organized in chapters by category of disease with a separate chapter for skeletal muscle. Many of the diseases could be included in more than one chapter because of overlapping pathophysiology; in each case the disorder is included in a single section in the interest of convenience. In order to recognize pathology one must have a basic foundation in normal structure, so the first chapter is an overview of basic regional central nervous system structure and anatomy. It includes an introduction to neurohistology. Other chapters address the pathophysiology of different categories of disease and provide examples of gross and microscopic pathology when they are available. anatomy, central nervous system, disease, gross pathology, microscopic pathology, neurohistology, neuropathology, pathology, pathophysioogy, skeletal muscle, structure Free, Freely available nif-0000-10438 http://www.stonybrookmedicalcenter.org/body.cfm?id=1176 SCR_001866 SciCrunch Registry Neuropathology Primer 2026-10-17 01:25:10 0
SPRUSTON / KATH LAB: Neuraling Modeling Database NEURAL MODELING DATABASE
 
Resource Report
Resource Website
1+ mentions
SPRUSTON / KATH LAB: Neuraling Modeling Database NEURAL MODELING DATABASE (RRID:SCR_001869) data or information resource, database, simulation software, software application, software resource This database contains morphologies of hippocampal pyramidal cells and interneurons (in Neurolucida, NEURON, and pdf formats) as well as data recorded from those cells. Sponsors:This work was supported by grants from the NIH (T32-GM-08061 to T.J.M., F32-NS-10532 to N.L.G., and R01-NS35180 and R01-NS 46064 to N.S. and W.L.K.) and NSF (IGERT fellowship to Y.K.). NS46064 is part of the NSF/NIH Collaborative Research in Computational Neuroscience Program cell, hippocampal, interneuron, morphology, neurolucida, neuron, pyramidal cell Free, Freely available nif-0000-10434 http://www.northwestern.edu/neurobiology/faculty/spruston/sk_models/ SCR_001869 SciCrunch Registry SPRUSTON / KATH LAB 2026-10-17 01:25:02 5
Korea Advanced Institute of Science and Technology; Daejeon; South Korea
 
Resource Report
Resource Website
1+ mentions
Korea Advanced Institute of Science and Technology; Daejeon; South Korea (RRID:SCR_001902) KAIST institution Institute dedicated to research in science and technology in South Korea modeled after a research university. south korea, research, science, technology is parent organization of: NIRS-SPM
is parent organization of: FiGS
Available to the research community grid.37172.30, ISNI: 0000 0001 2292 0500, Crossref funder ID: 501100007107, Wikidata: Q39949, nlx_155859 https://ror.org/05apxxy63 http://www.kaist.edu/english/ SCR_001902 SciCrunch Registry Korea Advanced Institute of Science and Technology 2026-10-17 01:25:27 2

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