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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
NVivo Resource Report Resource Website 10000+ mentions |
NVivo (RRID:SCR_014802) | data analysis software, software application, data processing software, software resource | Software suite for qualitative data analysis for text-based data and higher-order forms of data. Various packages are available and are dependent on the system used and the type of data analysis needed. | qualitative, data analysis, software, data solution | is listed by: SoftCite | SCR_014802 | 2026-02-17 10:02:44 | 11593 | |||||||||||
|
ProtTest Resource Report Resource Website 1000+ mentions |
ProtTest (RRID:SCR_014628) | software application, web application, data processing software, data analysis software, software resource | Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bioinformatics, model, best fit model, protein evolution, amino acid replacement, server, bio.tools |
uses: PhyML is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is hosted by: GitHub |
PMID:15647292 DOI:10.1093/bioinformatics/btr088 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11547, biotools:prottest | https://github.com/ddarriba/prottest3 https://bio.tools/prottest https://sources.debian.org/src/prottest/ |
SCR_014628 | 2026-02-17 10:02:43 | 1981 | |||||||
|
IUPRED Resource Report Resource Website 100+ mentions |
IUPRED (RRID:SCR_014632) | software application, web application, data processing software, data analysis software, software resource, sequence analysis software | A web server which recognizes tertiary structures from an amino acid sequence based on estimated pairwise energy content. Users can input SWISS-PROT/TrEMBL identifier or accession number, or paste the amino acid sequence. | web application, sequence analysis, web server, territory structure, amino acid sequence, swiss prot, trembl | is listed by: SoftCite | PMID:15955779 | Available to academic users, Available for download, Commercial users must enquire | SCR_014632 | Prediction of Intrinsically Unstructured Proteins, Prediction of Intrinsically Unstructured Proteins (IUPRED) | 2026-02-17 10:02:15 | 295 | ||||||||
|
FastQC Resource Report Resource Website 10000+ mentions Rating or validation data |
FastQC (RRID:SCR_014583) | data management software, software application, data processing software, data analysis software, software resource | Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis. | quality control, sequence data, sequencing, analysis, data quality, pipeline, raw sequence data, modular set, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Open source, Available for download | biotools:fastqc, SCR_005539, OMICS_01043 | https://omictools.com/fastqc-tool https://bio.tools/fastqc https://sources.debian.org/src/fastqc/ |
SCR_014583 | FastQC v0.11.5 | 2026-02-17 10:02:51 | 18745 | |||||||
|
Brain Extraction Tool Resource Report Resource Website 10+ mentions |
Brain Extraction Tool (RRID:SCR_014586) | BET2, BET | image processing software, software application, data processing software, software resource | Software tool which deletes non-brain tissue from image of the whole head and estimates both internal and external skull surfaces. | delete non-brain tissue from image, whole head, internal and external skull surfaces estimation, |
is listed by: SoftCite is a plug in for: FSL |
Free, Freely available | http://poc.vl-e.nl/distribution/manual/fsl-3.2/bet2/ | SCR_014586 | Brain Extraction Tool (BET), Brain Extraction Tool (BET2) | 2026-02-17 10:02:14 | 16 | |||||||
|
Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | alignment software, software application, data processing software, data analysis software, software resource, sequence analysis software, image analysis software | Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. | sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: HLA-HD is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Bowtie |
NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:22388286 | Free, Available for download, Freely available | biotools:bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml https://github.com/BenLangmead/bowtie2 https://bio.tools/bowtie2 |
SCR_016368 | , bowtie 2, bowtie2 v 2.2.3 | 2026-02-17 10:02:44 | 1745 | |||||
|
WinWCP Resource Report Resource Website 100+ mentions |
WinWCP (RRID:SCR_014713) | software application, data processing software, data analysis software, data acquisition software, software resource | Windows software program for recording and analyzing signals from whole cell voltage and current clamp experiments. Its features include automatic waveform measurement, quantal content analysis, command voltage pulse generation, and spontaneous event detection. | data analysis software, whole cell, voltage, current, clamp experiments, neuron, neuroinformatics, single cell recording |
is listed by: SoftCite is affiliated with: Strathclyde Electrophysiology Suite |
Open source for academic and non-profit use, License available for purchase for commercial organizations | SCR_014713 | Windows Whole Cell Program | 2026-02-17 10:02:16 | 412 | |||||||||
|
PAUP Resource Report Resource Website 1000+ mentions |
PAUP (RRID:SCR_014931) | PAUP | software application, data processing software, data analysis software, software resource, data visualization software | Software which creates phylogenetic trees from molecular, morphological and/or behavioral data through high speed computer analysis. | phylogenetic tree, phylogeny, evolutionary tree, molecular data, morphological data, behavioral data |
is listed by: SoftCite works with: PAML |
Free | http://people.sc.fsu.edu/~dswofford/paup_test/ | SCR_014931 | Phylogenetic Analysis Using Parsimony | 2026-02-17 10:02:45 | 2266 | |||||||
|
Statgraphics Centurion Resource Report Resource Website 1+ mentions |
Statgraphics Centurion (RRID:SCR_015248) | software application, data processing software, data analysis software, software resource, data visualization software | Data analysis and visualization software with features that include a R interface, demographic maps, bivariate density estimation, multiple time series visualization, repeated ANOVA measures, and a multivariate visualizers. | statistical analysis software, statistical visualization software, statistical analysis | is listed by: SoftCite | Available for download, Trial available, Available for purchase | SCR_015248 | Statgraphics Centurion XVII | 2026-02-17 10:03:09 | 7 | |||||||||
|
MetaboAnalyst Resource Report Resource Website 10000+ mentions |
MetaboAnalyst (RRID:SCR_015539) | data access protocol, production service resource, analysis service resource, service resource, software resource, web service, data analysis service | Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification. | statistical, functional, integrative, analysis, metabolomics, data, processing, annotation, biomarker, discovery |
is listed by: SoftCite has parent organization: McGill University; Montreal; Canada has parent organization: University of Alberta; Alberta; Canada |
Alberta Ingenuity Fund ; Alberta Life Sciences Institute ; Canadian Institutes for Health Research ; Genome Alberta ; McGill University ; Natural Sciences and Engineering Research Council of Canada ; Genome Canada ; Canada Research Chairs Program |
PMID:29762782 | Free, Available for download, Freely available, Tutorial available, Acknowledgement requested | SCR_016717 | http://old.metaboanalyst.ca/MetaboAnalyst/ | SCR_015539 | MetaboAnalyst 4.0, MetaboAnalyst 3.0 | 2026-02-17 10:02:52 | 10983 | |||||
|
X!Tandem Resource Report Resource Website 10+ mentions |
X!Tandem (RRID:SCR_015645) | data analysis software, software application, data processing software, software resource | Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences. | Search engine, command line tool, matching tandem mass spectra, peptide sequence, protein sequence, protein identification, tandem mass spectrum, xml file, FASEB list |
is listed by: SoftCite is related to: XTandem Parser |
Free, Available for download, Freely available | SCR_018388 | SCR_015645 | 2026-02-17 10:02:53 | 44 | |||||||||
|
JASP Resource Report Resource Website 1000+ mentions |
JASP (RRID:SCR_015823) | data analysis software, software application, data processing software, software resource | Statistics software that performs common frequentist analyses and Bayesian analyses. It conducts ANOVA, linear regression, and correlation, among other statistical tests. | statistical analysis, data analysis, statistical test, frequentist analysis, bayesian analysis, r package |
uses: R Project for Statistical Computing is listed by: SoftCite |
European Research Council | PMID:28685272 | Open source, Free, Available for download, Tutorial available, Runs on Windows, Runs on MAC OS, Runs on Linux | https://github.com/jasp-stats/jasp-desktop | SCR_015823 | 2026-02-17 10:03:19 | 3851 | |||||||
|
MCODE Resource Report Resource Website 1000+ mentions |
MCODE (RRID:SCR_015828) | software application, data processing software, algorithm resource, data analysis software, software resource, image analysis software | Software that clusters a given network based on topology to find densely connected regions. It can be used to find protein complexes and parts of pathways in protein-protein interaction networks or protein families in protein similarity networks. | cluster, clustering, graph analysis, network, network topology, interconnectivity | is listed by: SoftCite | Canadian Institutes of Health Research (CIHR) ; Ontario Research and Development Challenge Fund ; MDS-Sciex |
PMID:12525261 PMID:25570063 |
Free, Available for download | http://baderlab.org/Software/MCODE | SCR_015828 | 2026-02-17 10:02:37 | 1150 | |||||||
|
Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | software application, data processing software, data analysis software, sequence analysis software, software resource, software toolkit | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | 2026-02-17 10:02:55 | 81 | ||||||
|
Metscape Resource Report Resource Website 100+ mentions |
Metscape (RRID:SCR_014687) | resource, source code, software resource | A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data. | metabolomics, metabolomics tool, visualization, expression profiling, gene, compound, metabolism, human |
is listed by: Metabolomics Workbench is listed by: SoftCite |
NIDDK U24 DK097153; NIDDK P30DK089503 |
PMID:22135418 | Freely available | SCR_014687 | 2026-02-17 10:02:16 | 145 | ||||||||
|
MINC Resource Report Resource Website 100+ mentions |
MINC (RRID:SCR_002391) | MINC | image analysis software, software application, data processing software, software resource | A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction. | reusable library, c, file format, fortran, information specification, minc, minc2, magnetic resonance, os independent, perl, sh/bash, unix shell |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite is related to: MINC Example files is related to: Extensible MATLAB Medical image Analysis has parent organization: McConnell Brain Imaging Center |
Free, Available for download, Freely available | nlx_155794 | http://www.nitrc.org/projects/minc | SCR_002391 | MINC - Medical Image NetCDF, Medical Imaging NetCDF | 2026-02-17 09:59:55 | 122 | ||||||
|
EEGLAB Resource Report Resource Website 5000+ mentions |
EEGLAB (RRID:SCR_007292) | EEGLAB | software application, data processing software, software resource, software toolkit | Interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data. First developed on Matlab 5.3 under Linux, EEGLAB runs on Matlab v5 and higher under Linux, Unix, Windows, and Mac OS X (Matlab 7+ recommended). EEGLAB provides an interactive graphic user interface (GUI) allowing users to flexibly and interactively process their high-density EEG and other dynamic brain data using independent component analysis (ICA) and/or time/frequency analysis (TFA), as well as standard averaging methods. EEGLAB also incorporates extensive tutorial and help windows, plus a command history function that eases users'' transition from GUI-based data exploration to building and running batch or custom data analysis scripts. EEGLAB offers a wealth of methods for visualizing and modeling event-related brain dynamics, both at the level of individual EEGLAB ''datasets'' and/or across a collection of datasets brought together in an EEGLAB ''studyset.'' For experienced Matlab users, EEGLAB offers a structured programming environment for storing, accessing, measuring, manipulating and visualizing event-related EEG data. For creative research programmers and methods developers, EEGLAB offers an extensible, open-source platform through which they can share new methods with the world research community by publishing EEGLAB ''plug-in'' functions that appear automatically in the EEGLAB menu of users who download them. For example, novel EEGLAB plug-ins might be built and released to ''pick peaks'' in ERP or time/frequency results, or to perform specialized import/export, data visualization, or inverse source modeling of EEG, MEG, and/or ECOG data. EEGLAB Features * Graphic user interface * Multiformat data importing * High-density data scrolling * Defined EEG data structure * Open source plug-in facility * Interactive plotting functions * Semi-automated artifact removal * ICA & time/frequency transforms * Many advanced plug-in toolboxes * Event & channel location handling * Forward/inverse head/source modeling | visualization, eeg modeling, independent component analysis, meg modeling, eeg, erp, spectral decomposition, single-trial, matlab, meg, electrophysiology, format conversion, source separation analysis, fourier time-domain analysis, spectral analysis, temporal wavelet analysis, anova, event related potential, three dimensional display, two dimensional display |
uses: ERPwavelab is used by: PeriodAmplitudeAnalysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: SoftCite is related to: Neural Maestro is related to: Measure Projection Toolbox is related to: NFT is related to: Source Information Flow Toolbox is related to: HeadIT is related to: BCILAB is related to: EEGVIS is related to: EYE-EEG (combined eye-tracking & EEG) is related to: Libeep EEGLAB plugin is related to: The Bergen fMRI Toolbox Plugin for EEGLab is related to: BVA import/export EEGLAB plugin has parent organization: Swartz Center for Computational Neuroscience has plug in: Dusk2Dawn works with: FieldTrip |
NINDS | PMID:15102499 | Free, Available for download, Freely available | nif-0000-00076 | https://eeglab.org/others/EEGLAB_References.html | http://www.nitrc.org/projects/incf_eeglab/, http://sccn.ucsd.edu/eeglab/index.html | SCR_007292 | 2026-02-17 10:01:12 | 6721 | ||||
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V3D Resource Report Resource Website 1+ mentions |
V3D (RRID:SCR_008646) | V3D | data visualization software, software application, data processing software, d visualization software, software resource, segmentation software, image analysis software | V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily. | 3d, annotation, bioimage, brain, cell, development, informatics, neuron, registration, segmentation, software, tracing, visual, visualization, image |
is listed by: SoftCite has parent organization: Janelia Research |
Howard Hughes Medical Institute | PMID:20231818 | nif-0000-32975 | SCR_008646 | V3D: A Swiss army knife for bioimage visualization & analysis | 2026-02-17 10:01:09 | 3 | ||||||
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FASTA Resource Report Resource Website 500+ mentions |
FASTA (RRID:SCR_011819) | FASTA | software application, data processing software, data analysis software, software resource, sequence analysis software | Software package for DNA and protein sequence alignment to find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. | sequence, alignment, DNA, protein, similarity, searching |
is listed by: OMICtools is listed by: SoftCite has parent organization: European Bioinformatics Institute |
Free, Freely available | OMICS_00994 | SCR_011819 | Federal Acquisition STreamlining Act | 2026-02-17 10:01:58 | 845 | |||||||
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CMap Resource Report Resource Website 100+ mentions |
CMap (RRID:SCR_016204) | web application, data or information resource, database, software resource, data set | Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines. | data, set, connectivity, gene, expression, database, heat map, drug, tool, perturbational, perturbagen, signature, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Free for academic use, Subscription for commercial use, Available for download, Acknowledgement requested | biotools:CMap | https://bio.tools/CMap | SCR_016204 | LINCS CMap L1000, LINCS L1000, LINCS CMap, ConnectivityMap, Connectivity Map | 2026-02-17 10:02:40 | 483 |
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