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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Scalpel Resource Report Resource Website 50+ mentions |
Scalpel (RRID:SCR_012107) | software resource | A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina). | software package, c++, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25128977 | biotools:scalpel, OMICS_05395 | https://bio.tools/scalpel | SCR_012107 | 2026-09-05 06:27:20 | 62 | ||||||||
|
xMSanalyzer Resource Report Resource Website 50+ mentions |
xMSanalyzer (RRID:SCR_012144) | software resource | A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat. | software package, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23323971 | GNU General Public License | OMICS_06039 | SCR_012144 | 2026-09-05 06:27:21 | 90 | ||||||||
|
freesurfR Resource Report Resource Website |
freesurfR (RRID:SCR_014110) | data analysis software, data processing software, software application, software resource, software toolkit | A software package which contains tools for doing group analysis of FreeSurfer surface data using the general linear model in R (lm). Results can be rendered in FreeSurfer freeview or AFNI SUMA. Plots for selected vertices can be rendered in R with ggplot2. | data analysis software, software package, group analysis, freesurfer, surface data, r linear model |
uses: FreeSurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Available for download | SCR_014110 | 2026-09-05 06:27:43 | 0 | ||||||||||
|
minc-toolkit Resource Report Resource Website 1+ mentions |
minc-toolkit (RRID:SCR_014138) | data processing software, image processing software, software application, software resource, software toolkit | A set of MINC-based image processing tools packaged together. It includes MINC, N3, BICPL, EBKTS, ANIMAL, INSECT, BEaST, Register, Display, and xdisp. | image processing, software package |
uses: minc-toolkit-testsuite is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
Available to the research community | http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit, https://github.com/BIC-MNI/minc-toolkit | SCR_014138 | MINC Tool Kit | 2026-09-05 06:27:43 | 9 | ||||||||
|
HAMMER: Deformable Registration Resource Report Resource Website |
HAMMER: Deformable Registration (RRID:SCR_014118) | data processing software, image processing software, software application, software resource | A software package which performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements. | image processing, software package, warp, brain image | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available for download | SCR_014118 | 2026-09-05 06:27:43 | 0 | ||||||||||
|
Olympus Cell Software Resource Report Resource Website 10+ mentions |
Olympus Cell Software (RRID:SCR_014342) | data acquisition software, data analysis software, data processing software, software application, software resource, software toolkit | A collection of 7 individual software packages that all control the Olympus Imaging systems while also providing different individual features including (but not limited to): basic measurement functions, process automation, ratio analysis, and real time image acquisition. | software package, data analysis, data acquisition, real time, automation | is provided by: Olympus | Exclusive distributor for Greece, Pay for product, Only for Olympus Imaging systems | SCR_014342 | 2026-09-05 06:27:45 | 16 | ||||||||||
|
Mascot Resource Report Resource Website 5000+ mentions |
Mascot (RRID:SCR_014322) | data processing software, signal processing software, software application, software resource, standalone software | A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters. | server, software package, mass spectrometry, protein, identify, characterize, bio.tools |
is used by: MSQuant is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: MascotScan |
Free, Can be licensed for in-house use, Available for download | biotools:MASCOT | http://www.matrixscience.com/search_intro.html, https://bio.tools/MASCOT | SCR_014322 | Mascot Server | 2026-09-05 06:27:45 | 7141 | |||||||
|
Hierarchical Attribute Matching Mechanism for Elastic Registration Resource Report Resource Website 50+ mentions |
Hierarchical Attribute Matching Mechanism for Elastic Registration (RRID:SCR_001960) | HAMMER | data processing software, software application, software resource | Software package that performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements. In order to make HAMMER as robust as possible to different acquisition protocols and conditions, they provide a distribution that assumes that images have been skull-stripped and segmented into gray matter, white matter, and ventricular CSF. We have other software tools that can perform these steps, including skull stripping, reorientation and reslicing, and segmentation tools. Importantly, they use 250 for WM, 150 for GM, 50 for Ventricles and 10 for CSF in the tissue-segmented brain images. Current modules used for group analysis: Labeling subject brain using a manually-labeled brain Model; Generating RAVENS map for each tissue (WM, GM, VN); Normalizing subject brain images | magnetic resonance, software package, data processing, high dimensional warping |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania; Philadelphia; USA |
PMID:12575879 PMID:12507441 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00310 | http://www.nitrc.org/projects/hammerwml | SCR_001960 | HAMMER: Deformable Registration | 2026-09-05 06:30:37 | 50 | |||||
|
Brainvox Resource Report Resource Website 1+ mentions |
Brainvox (RRID:SCR_009448) | data processing software, image analysis software, software application, software resource | An interactive 3D rendering and neuroanatomical analysis package developed for analyzing focal brain lesions and functional brain imaging data (Damasio and Frank, 1991; Frank, Damasio and Grabowski, 1997). | magnetic resonance, neuroanatomical analysis, software package, 3d, interactive, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
PMID:9038281 | Available for download | nlx_155592 | SCR_009448 | 2026-09-05 06:30:45 | 1 | ||||||||
|
BROCCOLI Resource Report Resource Website 10+ mentions |
BROCCOLI (RRID:SCR_014093) | data processing software, image analysis software, software application, software resource | A software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. If BROCCOLI is running on a GPU, it can perform non-linear spatial normalization to a 1 mm brain template in 4-6 s and run a second level permutation test with 10,000 permutations. | software package, parallel analysis, fmri, non linear spatial normalization, brain | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | https://github.com/wanderine/BROCCOLI/ | SCR_014093 | 2026-09-05 06:30:48 | 22 | |||||||||
|
clValid Resource Report Resource Website 50+ mentions |
clValid (RRID:SCR_014626) | data analysis software, data processing software, software application, software resource | An R package which contains functions for validating the results of a clustering analysis. | data analysis software, r, software package, cluster, cluster analysis, validation, results validation | is related to: CRAN | https://cran.r-project.org/web/packages/clValid/clValid.pdf | SCR_014626 | clValid - Validation of Clustering Results, clValid: Validation of Clustering Results | 2026-09-05 06:27:49 | 86 | |||||||||
|
GROMACS Resource Report Resource Website 5000+ mentions |
GROMACS (RRID:SCR_014565) | simulation software, software application, software resource, software toolkit | Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers. | simulation, molecular dynamics, software package, software toolkit, biochemical, molecule, protein, lipid, nucleic acid, bond interaction, bio.tools |
is used by: CHARMM-GUI is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ; Nvidia ; Stream Computing Performance Engineers ; Swedish eScience Research Center ; Swedish Foundation for International Cooperation in Research and Higher Education ; Swedish Foundation for Strategic Research ; Swedish National Infrastructure for Computing ; Swedish Research Council |
PMID:26620784 DOI:10.1016/0010-4655(95)00042-E |
Free, Available for download | biotools:gromacs, OMICS_05081 | https://bio.tools/gromacs, https://sources.debian.org/src/gromacs/, https://github.com/gromacs/gromacs | SCR_014565 | Gromacs | 2026-09-05 06:27:48 | 9367 | |||||
|
Analysis and Annotation Tool (AAT) Package Resource Report Resource Website 1+ mentions |
Analysis and Annotation Tool (AAT) Package (RRID:SCR_014658) | data analysis software, data processing software, software application, software resource | Genome tool for analyzing and annotating large genomic sequences containing introns. It includes a program for comparing the query sequence with a protein database and another for comparing the query with a cDNA database. The database search program identifies regions of the query sequence that are similar to a database sequence. Then the alignment program constructs an optimal alignment for each region and the database sequence, as well as reports the coordinates of exons in the query sequence. Pairwise alignments of the query sequence with protein and cDNA database sequences are combined into multiple sequence alignments, which provide a view of all protein and cDNA sequences matching a query region. | data analysis, software package, genome tool, genomic sequences, query sequence, protein database, cdna database | Available for download | SCR_014658 | Analysis and Annotation Tool Package, AAT Package | 2026-09-05 06:27:49 | 1 | ||||||||||
|
LeadIT Resource Report Resource Website 100+ mentions |
LeadIT (RRID:SCR_014881) | software resource | Drug discovery platform for medicinal and computational researchers. Users can assess the binding affinity and contributions to binding of a complex, find new scaffolds, grow molecules towards pharmacophore points, link fragments, and investigate possible dock binding conformations. | drug discovery, platform, binding, docking, complex, small molecule, software package, drug design | License must be purchased, Older versions are available | SCR_014881 | 2026-09-05 06:27:51 | 151 | |||||||||||
|
MOE Resource Report Resource Website 10+ mentions |
MOE (RRID:SCR_014882) | software resource | Drug discovery software package which can be used in structure-based design, fragment-based design, pharmacophore discovery, medicinal chemistry, protein and antibody modelling, and molecular modeling and simulations. Each aspect of the software package has its own unique features: for example, features for structure-based design include active site detection, scaffold replacement, multi fragment search, and solvent analysis. | drug discovery, software package, structure based design, fragment based design, pharmacophore, medicinal chemistry, protein modeling, antibody modeling, molecular modeling, molecular simulations | is listed by: SoftCite | SCR_014882 | 2026-09-05 06:27:51 | 27 | |||||||||||
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HKL 3000 Resource Report Resource Website 100+ mentions |
HKL 3000 (RRID:SCR_015023) | data acquisition software, data processing software, software application, software resource | Semi-automatic crystallographic data collection software that integrates data collection, data reduction, phasing and model building in a single software package. | crystallography, crystallographic data collection, software package, hardware management software | PMID:16855301 | License required | https://www.rigaku.com/en/products/protein/hkl3000r | SCR_015023 | HKL-3000, HLK3000, HKL 3000R, HKL-3000R, HKL3000R | 2026-09-05 06:27:53 | 182 | ||||||||
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RUVSeq Resource Report Resource Website 100+ mentions |
RUVSeq (RRID:SCR_006263) | software resource | Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. | software package, unix/linux, mac os x, windows, r, differential expression, preprocessing, rna-seq |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25150836 | Artistic License, v2 | OMICS_05652 | SCR_006263 | RUVSeq: Remove Unwanted Variation from RNA-Seq Data | 2026-09-05 06:25:49 | 481 | |||||||
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Prime Resource Report Resource Website 500+ mentions |
Prime (RRID:SCR_014887) | software application, software resource | Software package that uses homology modeling and fold recognition to make protein structure predictions. | software package, protein structure, protein strcuture prediction, homology modeling, fold recognition, drug design | is listed by: SoftCite | Commercial | SCR_014887 | 2026-09-05 06:32:59 | 691 | ||||||||||
|
topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software resource, software toolkit | Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. | r, go, go graph, local similarities, software tool, software package, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite works with: Gene Ontology is hosted by: Bioconductor |
Available for download | biotools:topgo | https://bio.tools/topgo | SCR_014798 | 2026-09-05 06:32:59 | 3080 | ||||||||
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ncdfFlow Resource Report Resource Website |
ncdfFlow (RRID:SCR_000009) | software resource | Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05617 | SCR_000009 | ncdfFlow: A package that provides ncdf based storage for flow cytometry data | 2026-09-07 08:55:13 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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