Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
BIAevaluation Software Resource Report Resource Website 100+ mentions |
BIAevaluation Software (RRID:SCR_015936) | data analysis software, data processing software, data visualization software, software application, software resource, standalone software | Analysis software for life science data. This software package is for presentation and evaluation of sensorgram data from real-time BIA analyses. | evaluation, life, science, bia, biacore, sensorgram, bia, analysis, real-time | Commercially Available, Available for purchase, License available for purchase | http://www.molecular-interactions.si/data/equipment/BIAeval3-AC.pdf | SCR_015936 | BIAevaluation Software Kit, BIAevaluation | 2026-09-12 12:58:32 | 459 | |||||||||
|
Pattern Component Modelling Toolbox Resource Report Resource Website 1+ mentions |
Pattern Component Modelling Toolbox (RRID:SCR_015891) | PCM | data analysis software, data processing software, software application, software resource | Software for a Bayesian approach for evaluating representational models that specify how complex patterns of neural activity relate to visual stimuli, motor actions, or abstract thoughts. PCM evaluates the ability of models to predict novel brain activity patterns and integrates over all possible activity profiles and computes the marginal likelihood of the data under the activity profile distribution specified by the representational model. | bayesian, representational, model, motor, abstract, visual, encoding, neural, imaging, activity, pattern, analysis, voxel | James McDonnell Foundation ; JSPS 15J03233; NSERC RGPIN-2016-04890 |
PMID:28843540 | Free, Available for download | SCR_015891 | Pattern component modeling (PCM), PCM Toolbox, Pattern Component Modeling toolbox for multivariate analysis | 2026-09-12 12:58:32 | 3 | |||||||
|
Ariba Resource Report Resource Website 100+ mentions |
Ariba (RRID:SCR_015976) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. | software, analysis, tool, sequence, antibiotic, resistance, assembly, local, mlst |
is listed by: Debian is listed by: OMICtools |
Biotechnology and Biological Sciences Research Council BB/M014088/1; Wellcome Trust 206194 |
PMID:29177089 DOI:10.1099/mgen.0.000131 |
Free, Available for download, Freely available | OMICS_17327 | https://sources.debian.org/src/artemis/ | SCR_015976 | 2026-09-12 12:58:33 | 220 | ||||||
|
Autogrid Resource Report Resource Website 1000+ mentions |
Autogrid (RRID:SCR_015982) | data analysis software, data processing software, simulation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock. | software, automated, docking, analysis, tool, precalculate, set, grid, ligand, protein, target, molecular, simulation, modeling, protein-ligand interaction, data |
is listed by: SoftCite is related to: AutoDock has parent organization: The Scripps Research Institute Labs and Facilities |
The Scripps Research Institute ; San Diego ; California |
PMID:16862531 | THIS RESOURCE IS NO LONGER IN SERVICE | http://mgl.scripps.edu/forum | SCR_015982 | Autogrid toolkit, Autogrid: automated grid | 2026-09-12 12:58:33 | 1261 | ||||||
|
Atac Resource Report Resource Website 1000+ mentions |
Atac (RRID:SCR_015980) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences. | software, tool, DNA, sequence, analysis, aligning, genome, compare, mapping, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btr285 | Free, Freely available, Available for download | OMICS_29044, biotools:atac | https://bio.tools/atac, https://sources.debian.org/src/atac/ | SCR_015980 | 2026-09-12 12:58:33 | 1826 | |||||||
|
Axe Resource Report Resource Website 1+ mentions |
Axe (RRID:SCR_015984) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples. | software, tool, sequence, analysis, barcode, demultiplexing |
is listed by: Debian is listed by: OMICtools |
Free, Freely available, Available for download | OMICS_19788 | https://readthedocs.org/projects/axe-demultiplexer/, https://sources.debian.org/src/baitfisher/ | SCR_015984 | Axe-demultiplexer | 2026-09-12 12:58:33 | 1 | |||||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | data analysis software, data management software, data processing software, software application, software resource, software toolkit | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools, https://sources.debian.org/src/bamtools/ | SCR_015987 | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-09-12 12:58:33 | 344 | ||||||
|
Gannet Resource Report Resource Website 100+ mentions |
Gannet (RRID:SCR_016049) | data analysis software, data processing software, software application, software resource, source code | Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data. | mri, magnetic resonance spectroscopy, mrs, batch, analysis, matlab, neuroscience, brain | PMID:25548816 | https://www.nitrc.org/projects/gannet/, https://markmikkelsen.github.io/Gannet-docs/index.html | http://www.gabamrs.com/about | SCR_016049 | Gannet - Batch Analysis of Edited Magnetic Resonance Spectroscopy (MRS) Data | 2026-09-12 12:58:34 | 167 | ||||||||
|
MRTool Resource Report Resource Website 10+ mentions |
MRTool (RRID:SCR_015956) | data or information resource, portal, topical portal | Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12. | brain, imaging, neuroimaging, analysis, magnetic, resonance, mr | requires: SPM | DOI:10.1007/s12021-018-9355-3 | Free, Available for download, Runs on MAC OS, Runs on Windows | SCR_015956 | 2026-09-12 12:58:32 | 14 | |||||||||
|
scater Resource Report Resource Website 100+ mentions |
scater (RRID:SCR_015954) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data. | scRNA-seq, rna, rnaseq, single, cell, analysis, gene, expression, quality, control, preprocessing, normalization, visualization, r, bio.tools |
is listed by: Debian is listed by: bio.tools |
Cancer Research UK A17197; European Molecular Biology Laboratory ; National Health and Medical Research Council of Australia APP1112681; Oxford Single Cell Biology Consortium ; United Kingdom Medical Research Council |
Free, Available for download | biotools:scater | https://bioconductor.org/packages/scater/, https://bio.tools/scater | SCR_015954 | scater (single-cell analysis toolkit for gene expression data in R) | 2026-09-12 12:58:32 | 187 | ||||||
|
DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search. | sequence, aligner, high, performance, analysis, big, data, protein, DNA, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
PMID:25402007 DOI:10.1038/nmeth.3176 |
Free, Available for download | OMICS_08011, biotools:diamond | https://bio.tools/diamond, https://sources.debian.org/src/diamond-aligner/ | SCR_016071 | 2026-09-12 12:58:34 | 489 | |||||||
|
loadGtfToGe_db Resource Report Resource Website 1+ mentions |
loadGtfToGe_db (RRID:SCR_015998) | data processing software, data visualization software, software application, software resource | One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGtfToGe_db software loads GTF files to a database for Genome Explorer. It allows the user to browse the results through the GE. | analysis, pipeline, maser, genome, explorer, upload, database, browse | Ministry of Education ; Culture ; Sports ; Science and Technology ; Japan |
Restricted | http://cell-innovation.nig.ac.jp/maser_cgi/cip-pl_list_violin_en.cgi | SCR_015998 | Management and Analysis System for Enormous Reads: loadGtfToGe_db | 2026-09-12 12:58:33 | 1 | ||||||||
|
Datamash Resource Report Resource Website 1+ mentions |
Datamash (RRID:SCR_016067) | data analysis software, data processing software, software application, software resource | Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts. | command-line, interface, basic, numerical, textual, statistical, operation, input, data, files, automate, analysis, pipelines | is listed by: Debian | Free Software Foundation (FSF) | Free, Available for download | https://sources.debian.org/src/datamash/ | SCR_016067 | GNU Datamash | 2026-09-12 12:58:34 | 4 | |||||||
|
Good Calculators Resource Report Resource Website |
Good Calculators (RRID:SCR_017123) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web service as calculator for statistics and analysis. Used on variety of browsers as well as mobile and tablet devices.They include Z-score, sample size, t value, One Way ANOVA Calculator, Percentile Calculator, Chi Square, p Value, and more. | statistics, analysis, calculator | Free, Freely available | SCR_017123 | 2026-09-12 12:58:48 | 0 | |||||||||||
|
Bulked segregation analysis tools for outbreeding species Resource Report Resource Website 1+ mentions |
Bulked segregation analysis tools for outbreeding species (RRID:SCR_017009) | BSATOS | 1d time-series analysis software, data analysis software, data processing software, software application, software resource, time-series analysis software | Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data. | next, generation, sequencing, bulked, segregation, analysis, outbreeting, specie, gene, mapping, data | Free, Available for download, Freely available | SCR_017009 | Bulked segregation analysis tools for outbreeding species, Bulked Segregation Analysis Tools for Outbreeding Species, BSATOS | 2026-09-12 12:58:47 | 2 | |||||||||
|
mzStudio Resource Report Resource Website 1+ mentions |
mzStudio (RRID:SCR_017088) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool for proteomics data analysis, visualization, and notebook application. Dynamic digital canvas for user driven interrogation of mass spectrometry data. Operating system Unix/Linux, Windows. | proteomic, data, analysis, visualization, notebooking, mass, spectrometry, modification, gas, phase, fragmentation, behavior |
is listed by: OMICtools is related to: Python Programming Language |
Barr Program in Basic Research ; Dana-Farber Strategic Research Initiative ; Honorable Tina Brozman Foundation for Ovarian Cancer Research ; Michael J. Fox Foundation ; NCI CA042368; NCI CA178860; NCI CA188881 |
PMID:28763045 | Free, Available for download, Freely available | OMICS_26946 | https://omictools.com/mzstudio-tool | SCR_017088 | 2026-09-12 12:58:48 | 1 | ||||||
|
BRASS Resource Report Resource Website 10+ mentions |
BRASS (RRID:SCR_017091) | data analysis software, data processing software, software application, software resource | Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements. | analysis, BAM, file, paired, end, sequencing, determine, rearrangement, breakpoint, assemble |
is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | SCR_017091 | 2026-09-12 12:58:48 | 47 | ||||||||||
|
GenomeScope Resource Report Resource Website 500+ mentions |
GenomeScope (RRID:SCR_017014) | Genomescope | data analysis software, data processing software, service resource, software application, software resource | Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach. | genome, unassembled, sequenced, data, short, read, analysis, heterozygosity, repeat, content, size, kmer | is related to: Cold Spring Harbor Laboratory | NHGRI R01 HG006677; NSF DBI 1350041; NSF IOS 1237880 |
PMID:28369201 | Free, Freely available, | http://qb.cshl.edu/genomescope/ | SCR_017014 | 2026-09-12 12:58:47 | 800 | ||||||
|
miRTarVisPlus Resource Report Resource Website 1+ mentions |
miRTarVisPlus (RRID:SCR_017103) | miRTarVis+ | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web based interactive visual analytics tool for miRNA target predictions and integrative analyses of multiple prediction results. Used for sequence based miRNA target prediction by exploiting miRNA-mRNA expression profile data. | interactive, visual, analytical, miRNA, target, prediction, analysis, mRNA, expression, data | has parent organization: Seoul National University; Seoul; South Korea | Hankuk University of Foreign Studies Research Fund ; National Research Foundation of Korea |
PMID:28600227 | Free, Freely available | http://hcil.snu.ac.kr/research/mirtarvisplus | SCR_017103 | mirtarvisplus | 2026-09-12 12:58:48 | 3 | |||||
|
Ponemah Resource Report Resource Website 10+ mentions |
Ponemah (RRID:SCR_017107) | data acquisition software, data analysis software, data processing software, software application, software resource | Software tool for complete physiologic data acquisition and analysis used by physiologists, pharmacologists, and toxicologists to collect, analyze, and summarize preclinical study data. Allows to custom design configuration based on needs, budget and convenience without need for any programming. | Data Sciences International, Inc., physiologic, data, acquisition, analysis, collect, summerize, preclinical, custom, design | Available for purchase | SCR_017107 | 2026-09-12 12:58:48 | 23 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the kravitz2 Resources search. From here you can search through a compilation of resources used by kravitz2 and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that kravitz2 has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on kravitz2 then you can log in from here to get additional features in kravitz2 such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into kravitz2 you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
