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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FusionFinder Resource Report Resource Website 1+ mentions |
FusionFinder (RRID:SCR_011894) | FusionFinder | software resource | A perl-based software package, which can be used to find fusion transcript candidates in RNA-Seq data. | is listed by: OMICtools | OMICS_01349 | SCR_011894 | FusionHunter: identifying fusion transcripts using paired-end RNA-seq | 2026-07-25 12:07:24 | 4 | |||||||||
|
Guide Resource Report Resource Website 50+ mentions |
Guide (RRID:SCR_011903) | Guide | software resource | A desktop application for the bench biologists to analyse RNA-Seq and microarray expression data. It performs gene-centric analyses such as differential expression and pathways using well-established R modules, integrates data from multiple sources, and enables editing of R commands., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01405 | SCR_011903 | Guide: Application for gene expression analysis | 2026-07-25 12:07:23 | 63 | ||||||||
|
Oncofuse Resource Report Resource Website 10+ mentions |
Oncofuse (RRID:SCR_011904) | Oncofuse | software resource | Software tool designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells. |
is listed by: OMICtools is listed by: Debian |
DOI:10.1093/bioinformatics/btt445 | OMICS_01406 | https://sources.debian.org/src/oncofuse/ | SCR_011904 | 2026-07-25 12:07:24 | 14 | ||||||||
|
PRADA Resource Report Resource Website 10+ mentions |
PRADA (RRID:SCR_011906) | PRADA | software resource | A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01408, biotools:prada-rnaseq | https://bio.tools/prada-rnaseq | SCR_011906 | Pipeline for RNA-Sequencing Data Analysis | 2026-07-25 12:07:23 | 49 | |||||||
|
R-SAP Resource Report Resource Website 1+ mentions |
R-SAP (RRID:SCR_011907) | R-SAP | software resource | An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Georgia Institute of Technology; Georgia; USA |
OMICS_01409, biotools:r-sap | https://bio.tools/r-sap | http://www.mcdonaldlab.biology.gatech.edu/r-sap.htm | SCR_011907 | 2026-07-25 12:07:24 | 3 | |||||||
|
RobiNA Resource Report Resource Website 10+ mentions |
RobiNA (RRID:SCR_011908) | RobiNA | software resource | Software package for RNA-Seq-based transcriptomics. Used to analyse Illumina/Solexa-based RNA-Seq data, Affymetrix data and generic tabular two color or single channel array data. Offers variety of quality control methods that can be used to gain overview of experimental data technical quality and structure. | analyse Illumina/Solexa-based RNA-Seq data, data quality control, |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22684630 | OMICS_01411 | SCR_011908 | 2026-07-25 12:07:27 | 19 | ||||||||
|
RseqFlow Resource Report Resource Website 1+ mentions |
RseqFlow (RRID:SCR_011909) | RseqFlow | software resource | An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets. |
is listed by: OMICtools has parent organization: Google Code |
PMID:21795323 | OMICS_01412 | SCR_011909 | RseqFlow - An RNA-Seq analysis pipeline for Quality Control Expression Level Estimation Differentially Expressed Gene | 2026-07-25 12:07:23 | 2 | ||||||||
|
SHORE Resource Report Resource Website 100+ mentions |
SHORE (RRID:SCR_011863) | SHORE | software resource | A mapping and analysis pipeline for short read data produced on the Illumina platform. | is listed by: OMICtools | OMICS_01136 | SCR_011863 | 2026-07-25 12:07:23 | 157 | ||||||||||
|
ArrayMiner Resource Report Resource Website 1+ mentions |
ArrayMiner (RRID:SCR_011955) | ArrayMiner | software resource | A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01570, biotools:arrayminer | https://bio.tools/arrayminer | SCR_011955 | 2026-07-25 12:07:28 | 2 | ||||||||
|
Zeiss: libra 120 transmission electron microscope Resource Report Resource Website 1+ mentions |
Zeiss: libra 120 transmission electron microscope (RRID:SCR_016703) | instrument resource | Electron microscope by Carl Zeiss AG which combines flexibility and ease of use of new control electronics, Windows® based user interface and a vacuum system. | instrument, electron, microscope, Carl Zeiss | Commercially available | https://drive.google.com/file/d/1sgiYV8KlKkLXagtcEe1d-Oh7y0_GncP6/view?usp=drivesdk | https://www.binran.ru/files/ckp/tem/CKP_Libra%20120%20en_User%20Manual.pdf | SCR_016703 | Carl Zeiss AG - LIBRA 120, libra 120, The LIBRA 120 | 2026-07-25 12:08:27 | 1 | ||||||||
|
Gallios: Flow Cytometer Resource Report Resource Website 1+ mentions |
Gallios: Flow Cytometer (RRID:SCR_016702) | instrument resource | Instrument provides acquisition of up to 12 parameters with optical design for enhanced sensitivity for multicolor assays. With customized forward scatter, to achieve accurate size measurement, and optimized electronics for high resolution and fast, accurate processing for researchers needs. | instrument, coulter, flow, cytometer, multicolor, assay, cell, processing, parameter, acquisition | Commercially available | https://www.beckman.de/en/coulter-flow-cytometers/gallios/ | SCR_016702 | 2026-07-25 12:08:24 | 1 | ||||||||||
|
A-M SYSTEMS: Model 2100 Isolated Pulse Stimulator Resource Report Resource Website 1+ mentions |
A-M SYSTEMS: Model 2100 Isolated Pulse Stimulator (RRID:SCR_016677) | instrument resource | Instrument used for a variety of physiological stimulation protocols, including behavioral feedback, LTP/LTD, lesion making, electrode marking, ultrafast timing applications, orthodromic/antidromic stimulation, and kindling. Used in a neurophysiological and physiological experiment protocols. | A-M Systems, stimulation, instrument, neurophysiological, physiological, experiment, protocol | Commercially available | https://drive.google.com/file/d/1sN9NYzMciABPPgk09f3cVZDrhiJfak24/view?usp=drivesdk | https://www.a-msystems.com/pub/manuals/2100manual.pdf | SCR_016677 | 2026-07-25 12:08:26 | 6 | |||||||||
|
Columbus Instruments: Oxymax-CLAMS Resource Report Resource Website 100+ mentions |
Columbus Instruments: Oxymax-CLAMS (RRID:SCR_016718) | CLAMS | instrument resource | Instrumentation for monitoring behavior and physiology in lab animals by Columbus Instruments. Used for simultaneous multi parameter assessment of 1 to 32 test animals with automated operation for experiments lasting up to three days. | instrument, monitor, behavior, physiology, lab animal | Commercially available | https://physiology.case.edu/media/eq_manuals/eq_manual_clams_brochure.pdf | http://www.colinst.com/ | SCR_016718 | Comprehensive Lab Animal Monitoring System | 2026-07-25 12:08:24 | 456 | |||||||
|
BD Biosciences: FACSAria III Cell Sorter Resource Report Resource Website 50+ mentions |
BD Biosciences: FACSAria III Cell Sorter (RRID:SCR_016695) | instrument resource | Instrument for cell sorting by BD Biosciences where positive air pressure forces sample cell through an optically gel-coupled cuvette . Hydrodynamic focusing guides particles in a single-file stream through the cuvette, where laser light intercepts the stream at the sample interrogation point.Fluorescence activated cell sorting instrument. Flow cytometer as high speed fixed alignment benchtop cell sorter. Enables multicolor analysis of up to 13 fluorescent markers and two scatter parameters at time. | instrument, equipment, USEDit, BD Biosciences, cell, sorter, positive, air, pressure, force, cell, flow | is listed by: USEDit | Commercially available | https://drive.google.com/file/d/14L46Z9kYGpNi6KVjyhP9KmXogSN7q82n/view?usp=drivesdk | Model_Number_FACSAria_III | https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/BD-FACSAria-III-Cell-Sorter-Brochure.pdf, https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/FACSDiva_Software_Brochure.pdf | http://www.bdbiosciences.com/us/instruments/research/cell-sorters/bd-facsaria-iii/m/744763/features | SCR_016695 | BD FACSARIA III cell sorter, BD FACSARIA III | 2026-07-25 12:08:26 | 92 | |||||
|
Numbers Resource Report Resource Website 1+ mentions |
Numbers (RRID:SCR_016950) | software resource | Software tool to create spreadsheets that include tables and images. You can use Apple Pencil on your iPad to add diagrams and colorful illustrations. | Apple, create, spreadsheet, table, image, diagram, illustration, color | Commercially available | SCR_016950 | 2026-07-25 12:08:27 | 2 | |||||||||||
|
Whisker tracking macro Resource Report Resource Website 1+ mentions |
Whisker tracking macro (RRID:SCR_016953) | software resource | ImageJ plugins and macros for whisker tracking. Set of Fiji plugins and macros for tracking a single whisker. | ImageJ, plugin, macro, whisker, tracking, Fiji, single | is a plug in for: ImageJ | Free, Available for download, Freely available | SCR_016953 | 2026-07-25 12:08:27 | 2 | ||||||||||
|
Affinity Photo Resource Report Resource Website 10+ mentions |
Affinity Photo (RRID:SCR_016951) | software resource | Software tool for professional photo editing. | Affinity, professional, photo, editing | Commercially available | SCR_016951 | 2026-07-25 12:08:30 | 32 | |||||||||||
|
Olympus: FV1000 Confocal Microscope Resource Report Resource Website 10+ mentions |
Olympus: FV1000 Confocal Microscope (RRID:SCR_016840) | instrument resource | FV1000 confocal laser scanning biological microscope features twin scan system which enables spectroscopy of living intercellular contents and analysis of objects down to a 2nm wavelength resolution. Image size is increased to 4096x4096 pixels. | FV 1000, confocal, laser, scanning, microscope, spectroscopy, living, intercellular, object, Olympus | is provided by: Olympus | Commercially available | http://olympusconfocal.com/brochures/pdfs/FV1000.pdf | SCR_016840 | 2026-07-25 12:08:22 | 19 | |||||||||
|
Leica: CM3050 S Research Cryostat Resource Report Resource Website 10+ mentions |
Leica: CM3050 S Research Cryostat (RRID:SCR_016844) | instrument resource | Instrument designed for cryosectioning in biomedical, neuro-anatomical and pharmaceutical research. | instrument, cryosectioning, biomedical, neuroanatomical, cryostat, Leica, histology, equipment | Commercially available | https://www.leicabiosystems.com/sites/default/files/media_product-download/2022-01/Leica_CM3050S_IFU_2v4N_en.pdf | SCR_016844 | Leica CM3050 cryostat | 2026-07-25 12:08:25 | 23 | |||||||||
|
HBio: Multichallel Systems: Electro Square Porator ECM 830, BTX Resource Report Resource Website 1+ mentions |
HBio: Multichallel Systems: Electro Square Porator ECM 830, BTX (RRID:SCR_016841) | ECM 830 | instrument resource | ECM 830 is a square wave pulse generator designed for in vitro and in vivo applications for gene, drug and protein delivery for mammalian cells, zebra fish tissue and embryos, nuclear transfer, embryo manipulation, plant protoplast and basic bacteria and yeast transformations. Used in ECM 830 SQUARE WAVE ELECTROPORATION SYSTEM. | BTX, square, wave, pulse, generator, electroporation, ECM 830, transformation | Commercially available | https://drive.google.com/file/d/14QogTk99I1g4bW-H3N9obk7FYhxZbGjr/view?usp=drivesdk | https://www.btxonline.com/media/wysiwyg/tab_content/ECM_830.pdf | SCR_016841 | Electro Square Porator ECM 830, ECM 830, ECM 830 generator | 2026-07-25 12:08:25 | 4 |
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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."
