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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GobyWeb Resource Report Resource Website 1+ mentions |
GobyWeb (RRID:SCR_005443) | GobyWeb | software resource | Web application that facilitates the management and analysis of high-throughput sequencing (HTS) data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-Seq, Methyl-Seq, RRBS, or DNA-Seq datasets and to enable teams of investigators to share reads and results of analyses. GobyWeb can be extended for new analyses by developing plugins. | high-throughput sequencing, gene expression, dna methylation, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Weill Cornell Medical College; New York; USA |
PMID:23936070 | Acknowledgement requested, GNU Lesser General Public License, v3 | OMICS_00601, biotools:gobyweb | https://bio.tools/gobyweb | SCR_005443 | 2026-07-25 12:06:04 | 3 | ||||||
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QC-Chain Resource Report Resource Website 1+ mentions |
QC-Chain (RRID:SCR_005438) | QC-Chain | software resource | A software package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences. This QC pipeline supplies a fast, easy-to-use, and parallel processing approach to accomplish the comprehensive QC steps, which could be applied widely to almost all kinds of NGS reads, including genomic, transcriptomic and metagenomic data. | next generation sequencing |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
OMICS_01070 | SCR_005438 | 2026-07-25 12:06:03 | 4 | |||||||||
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VDJ Resource Report Resource Website 1+ mentions |
VDJ (RRID:SCR_005475) | software resource | Python package for analysing immune receptor sequences (antibodies and T cell receptors). | standalone software, python | is listed by: OMICtools | PMID:24639495 | Apache License, v2 | OMICS_04064 | SCR_005475 | 2026-07-25 12:06:04 | 3 | ||||||||
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CASHX Resource Report Resource Website 1+ mentions |
CASHX (RRID:SCR_005477) | CASHX | software resource | Software pipeline to parse, map, quantify and manage large quantities of sequence data. CASHX is a set of tools that can be used together, or as independent modules on their own. The reference genome alignment tools can be used with any reference sequence in fasta format. The pipeline was designed and tested using Arabidopsis thaliana small RNA reads generated using an Illumina 1G. |
is listed by: OMICtools has parent organization: Oregon State University; Oregon; USA |
NSF MCB-1231726; NIAI AI43288 |
PMID:19307293 | OMICS_00655 | SCR_005477 | Cache ASsisted Hash Search with Xor logic Pipeline, CASHX Pipeline, Cache ASsisted Hash Search with Xor logic | 2026-07-25 12:06:07 | 4 | |||||||
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QIAGEN Resource Report Resource Website 10000+ mentions |
QIAGEN (RRID:SCR_008539) | commercial organization | A commercial organization which provides assay technologies to isolate DNA, RNA, and proteins from any biological sample. Assay technologies are then used to make specific target biomolecules, such as the DNA of a specific virus, visible for subsequent analysis. | is parent organization of: Ingenuity Pathways Knowledge Base | nif-0000-31384 | SCR_008539 | QIAGEN | 2026-07-25 12:06:52 | 85828 | ||||||||||
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Q-Value Software Resource Report Resource Website 1+ mentions |
Q-Value Software (RRID:SCR_008538) | software resource | Features: * This software takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. A point-and-click interface is now available! * The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. * A short tutorial on q-values and false discovery rates is provided with the manual. * Various plots are automatically generated, allowing one to make sensible significance cut-offs. * Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. * The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining. This research was supported in part by a National Science Foundation graduate research fellowship. | has parent organization: Stanford University; Stanford; California | nif-0000-31382 | SCR_008538 | Q-Value Software | 2026-07-25 12:06:51 | 5 | ||||||||||
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Apache Tomcat Resource Report Resource Website 1+ mentions |
Apache Tomcat (RRID:SCR_008411) | software resource | Apache Tomcat is an open source software implementation of the Java Servlet and JavaServer Pages technologies. The Java Servlet and JavaServer Pages specifications are developed under the Java Community Process. Apache Tomcat is developed in an open and participatory environment and released under the Apache License version 2. Apache Tomcat is intended to be a collaboration of the best-of-breed developers from around the world. We invite you to participate in this open development project. Apache Tomcat powers numerous large-scale, mission-critical web applications across a diverse range of industries and organizations. Some of these users and their stories are listed on the PoweredBy wiki page. | software, technology, application, java | Yahoo ; Microsoft ; Google ; Facebook ; HP ; Basis Technology ; Covalent ; IONA ; AirPlus International ; BlueNog ; Intuit ; Joost |
nif-0000-30114 | SCR_008411 | Apache Tomcat | 2026-07-25 12:06:50 | 7 | |||||||||
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GEDI Resource Report Resource Website 50+ mentions |
GEDI (RRID:SCR_008530) | GEDI | software resource | A program that opens a new perspective to the analysis of microarray data (e.g., gene expression profiling). Unlike traditional gene clustering software, GEDI is primarily sample-oriented rather than gene-oriented. By treating each high-dimensional sample, such as one microarray experiment, as an object, it accentuates the genome-wide response of a tissue or a patient and treats it as an integrated biological entity. Hence, GEDI honors the new spirit of a system-level approach in biology. Yet, it also allows the researcher to quickly zoom-in from global patterns onto individual genes that exhibit interesting expression behavior and retrieve gene-specific information. Therefore, GEDI unites a novel holistic perspective with the traditional gene-centered approach in molecular biology. GEDI allows experimental biologists or clinicians with no bioinformatics background to efficiently and intuitively navigate through a large number of expression profiles, each with a memorizable face, and inspect, group and collect them, like managing a stack of baseball cards. DYNAMIC ANALYSIS: The unique strength of GEDI, for which GEDI was originally developed, is that it can display the results of parallel monitoring of multiple high-dimensional time courses, such as the comparison of expression profile time evolution in response to a series of drugs. GEDI creates animated graphics showing how 10,000s of genes change their expression over time in response to 100s of separately tested drugs. STATIC ANAYLSIS: The signature graphical output of GEDI, the GEDI-mosaics provide a unique, one-glance visual engram that gives each microarray or other high-dimensional dataset a face. A characteristic of GEDI''s analysis is that it does not prejudicate any particular structure in the data (such as clusters or hierarchical organization). Thus, it allows the researcher to use human pattern recognition to perform a global first-level analysis of the data. Sponsor. The project was supported by the Air Force Office of Scientific Research and the National Health Institutes. It is distributed for free academic use by the Childrens Hospital, Boston., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30604 | SCR_008530 | The Gene Expression Dynamics Inspector, Gene Expression Dynamics Inspector | 2026-07-25 12:06:51 | 73 | |||||||||
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Program DynaFit Resource Report Resource Website 100+ mentions |
Program DynaFit (RRID:SCR_008444) | software resource | Program DynaFit Analysis of (bio)chemical kinetics and equilibria Welcome to the DynaFit home page. Purpose Symbolic Notation Bibliographic Reference Numerical Methods Minimum System Requirements Purpose The main purpose of the program DynaFit is to perform nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data. The experimental data can be either initial reaction velocities in dependence on the concentration of varied species (e.g., inhibitor concentration vs. velocity), or the reaction progress curves (e.g., time vs. absorbance). Symbolic Notation The main advantage in using the program DynaFit is in the ability to characterize the (bio)chemical reacting system in terms of symbolic, or stoichiometric, equations. For example, the ``slow, tight'''' inhibition of a dissociative dimeric enzyme is described by the following text: Monomer Monomer <==> Enzyme : k1 k2 Enzyme Inhibitor <==> Complex : k3 k4 Enzyme Substrate <==> ReactiveX : k5 k6 ReactiveX --> Product Enzyme : k7 k8 The names of chemical species (Monomer, Enzyme, etc.) are entirely arbitrary and can be freely chosen by the investigator. Bibliographic Reference If you publish any results obtained by using DYNAFIT, plase cite the following reference: Kuzmic, P. (1996) Anal. Biochem. 237, 260-273. Program DYNAFIT for the Analysis of Enzyme Kinetic Data: Application to HIV Proteinase ABSTRACT A computer program with the code name DYNAFIT was developed for fitting either the initial velocities, or the time-course of enzyme reactions, to an arbitrary molecular mechanism represented symbolically by a set of chemical equations. Seven numerical tests and five graphical tests are applied to judge the goodness of fit. Experimental data on the inhibition of the dissociative dimeric proteinase from HIV were used in four test examples. A set of initial velocities was analyzed to see if a tight-binding inhibitor could bind to the HIV proteinase monomer. Three different sets of progress curves were analyzed (i) to determine the kinetic properties of an irreversible inhibitor; (ii) to investigate the dissociation and denaturation mechanism for the protease dimer; and (iii) to investigate the inhibition mechanism for a transient inhibitor. See a MEDLINE abstract with related references concerning the kinetics of HIV-1 protease. Numerical Methods The nonlinear regression module uses the Levenberg-Marquardt algorithm [1]. The time-course of (bio)chemical reactions is computed by the numerical integration of simultaous first-order ordinary differential equations, using the Livermore Solver of ODe Systems (LSODE, [2]). The composition of complex mixtures at equilibrium (e.g., in the concentration jump experiment where a complex mixture is incubated prior to the addition of a reagent) is computed by solving simultaneous nonlinear algebraic equations, namely, the mass balance equations for the component species, by using the multidimensional Newton-Raphson method [3]. References G. A. F. Seber and C. J. Wild (1989) Nonlinear Regression, Wiley, New York, p. 624. A. C. Hindmarsh (1983) ODEPACK: a systematized collection of ODE solvers; in Scientific Computing, ed. R. S. Stepleman et al., North Holland, Amsterdam, pp. 55--64. E. Kreyszig (1993) Advanced Engineering Mathematics; 7th ed., John Wiley, New York, p. 929. Minimum System Requirements DynaFit for Windows Intel Pentium III or Celeron class 800 MHz or faster processor Microsoft Windows XP (SP1) or 2000 (SP2) 128 MB RAM 20 MB Hard Disk Space Ethernet Network Interface Card required for license activation(1) CD/DVD-ROM drive required for software installation(2) (1) The Network Interface Card is used to compute a unique Computer ID, tied to a particular DynaFit license. Essentially the Computer ID required for license activation is an encrypted Media Access Control (MAC address) associated with the given Network Card. (2) CD/DVD-ROM is not required if the software is being installed by using the downloadable installer file dynafit-install.zip. Sponsor. This work has been supported by the NIH, grant No. R43 AI52587-02 and the U.S. Department of Defense, U.S. Army Medical Research and Materials Command, Ft. Detrick, MD, administered by the Pacific Telehealth & Technology Hui, Honolulu, HI, contract No. V549P-6073. | nif-0000-30477 | SCR_008444 | DynaFit | 2026-07-25 12:06:52 | 127 | |||||||||||
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Public Health Resources Unit Resource Report Resource Website 1+ mentions |
Public Health Resources Unit (RRID:SCR_008564) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Tools were developed by the Critical Appraisal Skills Programme (CASP) to help with the process of critically appraising articles of the following types of research. These are available and free to download for personal use. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31450 | http://www.sph.nhs.uk/what-we-do/public-health-workforce/resources/critical-appraisals-skills-programme | http://www.phru.nhs.uk/Pages/PHD/resources.htm | SCR_008564 | PHRU | 2026-07-25 12:06:51 | 1 | ||||||||
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LAGAN Resource Report Resource Website 50+ mentions |
LAGAN (RRID:SCR_008558) | software resource | About the LAGAN Toolkit The LAGAN Tookit consists of four components: CHAOS CHAOS is a pairwise local aligner optimized for non-coding, and other poorly conserved regions of the genome. It uses both exact matching and degenerate seeds, and is able to find homology in the presence of gaps. LAGAN LAGAN is our highly parametrizable pairwise global alignment program. It takes local alignments generated by CHAOS as anchors, and limits the search area of the Needleman-Wunsch algorithm around these anchors; Multi-LAGAN Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment. M-LAGAN performs progressive pairwise alignments, guided by a user-specified phylogenetic tree. Alignments are aligned to other alignments using the sum-of-pairs metric. Shuffle-LAGAN Shuffle-LAGAN is a novel glocal alignment algorithm that is able to find rearrangements (inversions, transpositions and some duplications) in a global alignment framework. It uses CHAOS local alignments to build a map of the rearrangements between the sequences, and LAGAN to align the regions of conserved synteny. The website uses scripts written by Alex Poliakov. The website was designed by Marina Sirota. | has parent organization: Stanford University; Stanford; California | DOI:10.1101/gr.926603 | OMICS_08469, nif-0000-31432 | https://sources.debian.org/src/lagan/ | SCR_008558 | LAGAN | 2026-07-25 12:06:49 | 82 | ||||||||
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SAFC Resource Report Resource Website 100+ mentions |
SAFC (RRID:SCR_008554) | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A business division of Sigma-Aldrich Corporation, focusing on providing custom manufactured products and specialized services used in the industrial development and manufacturing, including processes, that bring new drugs and new electronic products to market., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31481 | SCR_008554 | SAFC | 2026-07-25 12:06:53 | 380 | ||||||||||
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Classifier Visualization in R Resource Report Resource Website 10+ mentions |
Classifier Visualization in R (RRID:SCR_008551) | software resource | ROCR is a package for evaluating and visualizing the performance of scoring classifiers in the statistical language R. It features over 25 performance measures that can be freely combined to create two-dimensional performance curves. Standard methods for investigating trade-offs between specific performance measures are available within a uniform framework, including receiver operating characteristic (ROC) graphs, precision/recall plots, lift charts and cost curves. ROCR integrates tightly with R''s powerful graphics capabilities, thus allowing for highly adjustable plots. Being equipped with only three commands and reasonable default values for optional parameters, ROCR combines flexibility with ease of usage. Performance measures that ROCR knows: Accuracy, error rate, true positive rate, false positive rate, true negative rate, false negative rate, sensitivity, specificity, recall, positive predictive value, negative predictive value, precision, fallout, miss, phi correlation coefficient, Matthews correlation coefficient, mutual information, chi square statistic, odds ratio, lift value, precision/recall F measure, ROC convex hull, area under the ROC curve, precision/recall break-even point, calibration error, mean cross-entropy, root mean squared error, SAR measure, expected cost, explicit cost. ROCR features: ROC curves, precision/recall plots, lift charts, cost curves, custom curves by freely selecting one performance measure for the x axis and one for the y axis, handling of data from cross-validation or bootstrapping, curve averaging (vertically, horizontally, or by threshold), standard error bars, box plots, curves that are color-coded by cutoff, printing threshold values on the curve, tight integration with Rs plotting facilities (making it easy to adjust plots or to combine multiple plots), fully customizable, easy to use (only 3 commands). ROCR can be used under the terms of the GNU General Public License. Running within R, it is platform-independent. | has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany | PMID:16096348 | nif-0000-31415 | SCR_008551 | ROCR: Classifier Visualization in R, ROCR | 2026-07-25 12:06:53 | 15 | |||||||||
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Cython C-Extensions for Python Resource Report Resource Website 100+ mentions |
Cython C-Extensions for Python (RRID:SCR_008466) | software resource | Cython is a language that makes writing C extensions for the Python language as easy as Python itself. Cython is based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. The Cython language is very close to the Python language, but Cython additionally supports calling C functions and declaring C types on variables and class attributes. This allows the compiler to generate very efficient C code from Cython code. This makes Cython the ideal language for wrapping external C libraries, and for fast C modules that speed up the execution of Python code. Sponsor. Google and Enthought funded Dag Seljebotn to greatly improve Cython integration with NumPy. Kurt Smith and Danilo Freitas were funded through the Google Summer of Code program to work on improved Fortran and C support respectively. |
is related to: Python Programming Language is required by: TomoMiner |
nif-0000-30401 | SCR_008466 | Cython | 2026-07-25 12:06:48 | 135 | ||||||||||
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D. rerio Blast Server Resource Report Resource Website 1+ mentions |
D. rerio Blast Server (RRID:SCR_008461) | service resource | This Blast server offers searches against all D. rerio finished and unfinished clones in the Sanger sequencing pipeline. You can now also search the de novo assemblies generated from sequencing of one doubled haploid homozygous individual of each the AB and Tuebingen strain. Both fish were sequenced to ~40x coverage using Illumina GA sequencing technology and the sequences were assembled using Phusion2, resulting in a 1,33 Gb AB and a 1.48 Gb Tuebingen assembly. Due to the short reads and short inserts and no integration of physical or genetic map data, both assemblies are highly fragmented - with an N50 contig size of about 5kb. Mis-assembly errors may also be present in the contigs. Please note these assemblies are independent additions to the assemblies released by the zebrafish genome project and are intended to aid identification of polymorphisms between these two strains. Charity. Genome Research Limited is a charity registered in England with number 1021457 | has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom | nif-0000-30406 | SCR_008461 | D. rerio | 2026-07-25 12:06:52 | 6 | ||||||||||
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Rules Based Medicine Resource Report Resource Website 10+ mentions |
Rules Based Medicine (RRID:SCR_008575) | software resource | Rules-Based Medicine (RBM) uses proprietary Multi-Analyte Profiling (MAP) technology to make life science research and drug and diagnostic development programs more efficient and effective. Whether measuring hundreds of biomarkers or simply a few, our approach provides reproducible, quantitative immunoassay data from a small sample volume at a cost-effective price. RBM is CLIA certified and supports GLP studies. * Quality: All immunoassays are validated to clinical laboratory standards. This means complete validation for the clinic, not fit for purpose validation which at RBM means inferior validation. Learn More * Content: We have the most comprehensive menu of biomarker immunoassays available. * Small Sample Volumes: Multiplexing provides you with more data using a smaller sample volume. * Cost Effective: Multiplexing and automation combine to deliver high quality data at reasonable prices. * Ease of use: Ship us your samples and get results within 2 weeks. Rules-Based Medicine (RBM), the worlds leading multiplexed biomarker testing laboratory, provides comprehensive protein biomarker products and services based on its Multi-Analyte Profiling (MAP) technology platform. RBMs biomarker testing service provides pre-clinical and clinical researchers with reproducible, quantitative, multiplexed immunoassay data for hundreds of proteins in a cost-effective manner, from a small sample volume and from multiple species. Our biomarker testing laboratory is CLIA certified and supports GLP studies. Most diseases and drug effects manifest themselves in abnormal levels of specific biomarkers found in the peripheral blood. By providing multiplexed, quantitative, and reproducible tests for hundreds of biomarkers, RBM enables research that historically was not available due to sample volume requirements and associated costs. Use of our testing services can identify the sources of both the positive and negative effects of drugs during pre-clinical research and clinical trials. Biomarker testing results identify patients most likely to respond to a given therapy and the biochemical reason for that response, making clinical trials more successful and effective. Through its wholly owned subsidiary EDI GmbH, RBM provides Human Organo-Typic (HOT) cell culture systems. These co-culture systems consist of multiple primary cell types grown in a 3-D architecture that closely mimic particular human organs and are an ideal platform for ex vivo studies of drug safety and efficacy. RBM combines EDIs cell culture systems with its HumanMAP biomarker testing services to provide researchers with an unprecedented view of the physiological and biochemical impact of a new drug compound or consumer product prior to testing in a human subject. RBM also performs custom assay development, participates in co-sponsored research programs, and pursues in-licensing of novel high-value assays. | nif-0000-31474 | SCR_008575 | RBM | 2026-07-25 12:06:51 | 26 | |||||||||||
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Yahoo Developer Network Resource Report Resource Website 50+ mentions |
Yahoo Developer Network (RRID:SCR_008594) | software resource | The YUI Library is a set of utilities and controls, written with JavaScript and CSS, for building richly interactive web applications using techniques such as DOM scripting, DHTML and AJAX. YUI is available under a BSD license and is free for all uses. YUI is proven, scalable, fast, and robust. Built by frontend engineers at Yahoo! and contributors from around the world, it''s an industrial-strength JavaScript library for professionals who love JavaScript. | nif-0000-31921 | SCR_008594 | Yahoo | 2026-07-25 12:06:49 | 54 | |||||||||||
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WinLTP Resource Report Resource Website 100+ mentions |
WinLTP (RRID:SCR_008590) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Jan 16th 2025. WinLTP is a stimulation, data acquisition and on-line analysis electrophysiological software for studying Long-Term Potentiation (LTP), Long-term Depression (LTD), and related phenomena. WinLTP is multitasking and simultaneously runs 1) LTP stimulus/acquisition/analyzing sweeps with protocol scripting, and 2) continuous acquisition saving Axon Binary Files (abf). WinLTP runs on Windows PCI bus computers and uses National Instruments PCI M-Series boards and Axon Instruments'' Digidata 1320A and 1322A data acquisition boards. Other software that can use the M-Series boards includes Axograph Scientific''s AxoGraph X, WaveMetrics'' IGOR, National Instruments'' LabView, John Dempster''s Strathclyde Electrophysiology Suite (WinWCP and WinEDR), Silver lab''s Nclamp, and QUB data acquisition., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | has parent organization: University of Bristol; Bristol; United Kingdom | DOI:10.1016/j.jneumeth.2006.12.018 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31907 | SCR_008590 | WinLTP | 2026-07-25 12:06:49 | 218 | ||||||||
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Motif Extractor Resource Report Resource Website 100+ mentions |
Motif Extractor (RRID:SCR_008628) | software resource | motif-x (short for motif extractor) is a software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background. | has parent organization: Harvard University; Cambridge; United States | nif-0000-32002 | SCR_008628 | Motif-X | 2026-07-25 12:06:52 | 148 | ||||||||||
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DE-ID Data Corp Resource Report Resource Website 1+ mentions |
DE-ID Data Corp (RRID:SCR_008668) | software resource | A commercial organization that suppplies software which creates separate HIPAA-compliant repositories of de-identified patient records and reports. This software allows clinicians, researchers, and administrative leadership to safely access, search, share, and analyze de-identified patient-level data. DE-ID can be acquired as stand-alone tool or integrated with data networks or clinical information systems. | clinical, data, patient protection, surgical report | nif-0000-33387 | SCR_008668 | DE-ID Data Corp | 2026-07-25 12:06:52 | 1 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
