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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Proteome Discoverer Resource Report Resource Website 1000+ mentions |
Proteome Discoverer (RRID:SCR_014477) | data analysis software, data processing software, software application, software resource, workflow software | Software for identifying, characterizing, and quantifying proteins in biological samples. Can be used for range of proteomics workflows such as protein and peptide identification, PTM analysis, and isobaric mass tagging for quantification. Supports multiple database search algorithms and multiple dissociation techniques., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis, workflow software, proteomics, database search, FASEB list |
is used by: thermo-msf-parser is listed by: SoftCite works with: Peakjuggler works with: pepwheel |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014477 | 2026-09-12 12:58:17 | 1521 | ||||||||||
|
MaxQuant Resource Report Resource Website 10000+ mentions |
MaxQuant (RRID:SCR_014485) | data analysis software, data processing software, software application, software resource | A quantitative proteomics software package for analyzing large-scale mass-spectrometric data sets. It is a set of algorithms that include peak detection and scoring of peptides, mass calibration, database searches for protein identification, protein quantification, and provides summary statistics. | mass spectrometry analysis software, proteomics software, mass calibration, protein identification, protein quantification, FASEB list | is listed by: SoftCite | PMID:19029910 PMID:25059623 |
SCR_014485 | 2026-09-12 12:58:17 | 13452 | ||||||||||
|
Multi Gauge Resource Report Resource Website 10+ mentions |
Multi Gauge (RRID:SCR_014299) | data analysis software, data processing software, software application, software resource | A software application for one-dimensional electrophoretic analysis of multi-labeled fluorophores. It was designed to analyze multi-channel fluorescence data from Fujifilm FLA-5000 and FLA-8000 scanning systems. The software also works with other scanners in the BAS/FLA series and with the LAS series. | data analysis software, one dimensional electrophoretic analysis, fluorophore, multi channel fluorescence data | is listed by: SoftCite | http://www.scienceimaging.se/application-info/55.html | SCR_014299 | MultiGuage | 2026-09-12 12:58:15 | 37 | |||||||||
|
Clocklab Resource Report Resource Website 500+ mentions |
Clocklab (RRID:SCR_014309) | data acquisition software, data analysis software, data processing software, software application, software resource, standalone software | Point and click program used to quickly analyse circadian activity data using algorithms and embedded controls to make every graph interactive and useful for data analysis. The analysis program has been used for a variety of species including mice, hamsters, rats, sheep, Drosophila, and humans. This program has three separate applications: one for data collection, one for analysis, and a chamber control program. | circadian activity data, interactive, data analysis software, data acquisition software, standalone software | is listed by: SoftCite | Pay for product, Users can order different components of ClockLab separately | SCR_014309 | 2026-09-12 12:58:15 | 573 | ||||||||||
|
LabView Resource Report Resource Website 100+ mentions |
LabView (RRID:SCR_014325) | software application, software development environment, software development tool, software resource | A development environment for engineers and scientists to visualize, create, and code engineering systems. The system design software is integrated with all measurement hardware and contains signal processing IP. Other features include multithreaded execution, software deployment to hardware, and program integration into a single environment. | development environment, system design software, software development tool |
is used by: Demon Voltammetry and Analysis Software is listed by: SoftCite is related to: ZebEyeTrack is related to: ActiView |
Pay for product, Free trail is available | SCR_014325 | LabVIEW System Design Software, NI LabVIEW software, LabView System Design Software, LabVIEW | 2026-09-12 12:58:15 | 261 | |||||||||
|
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 | 2026-09-12 12:58:15 | 7141 | |||||||
|
ProtTest Resource Report Resource Website 1000+ mentions |
ProtTest (RRID:SCR_014628) | data analysis software, data processing software, software application, software resource, web application | 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 | 2026-09-12 12:58:19 | 1984 | |||||||
|
IUPRED Resource Report Resource Website 100+ mentions |
IUPRED (RRID:SCR_014632) | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | 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) | 2026-09-12 12:58:20 | 306 | ||||||||
|
FATCAT Resource Report Resource Website 100+ mentions |
FATCAT (RRID:SCR_014631) | software resource, web application | Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | web server, protein, comparison, structure, flexible protein structure, protein structure comparison, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: FATCAT Flexible Structural Neighborhood |
NIGMS GM101457; NIGMS GM63208; NIGMS GM076221; NSF DBI-0349600 |
PMID:14534198 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fatcat | https://bio.tools/fatcat | SCR_014631 | (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists, (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) | 2026-09-12 12:58:20 | 139 | |||||
|
FastQC Resource Report Resource Website 10000+ mentions Rating or validation data |
FastQC (RRID:SCR_014583) | data analysis software, data management software, data processing software, software application, 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 | 2026-09-12 12:58:18 | 19827 | |||||||
|
Brain Extraction Tool Resource Report Resource Website 10+ mentions |
Brain Extraction Tool (RRID:SCR_014586) | BET2, BET | data processing software, image processing software, software application, 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) | 2026-09-12 12:58:18 | 17 | |||||||
|
NVivo Resource Report Resource Website 10000+ mentions |
NVivo (RRID:SCR_014802) | data analysis software, data processing software, software application, 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 | 2026-09-12 12:58:22 | 13145 | |||||||||||
|
Simulink Resource Report Resource Website 100+ mentions |
Simulink (RRID:SCR_014744) | simulation software, software application, software resource, software toolkit | Block diagram environment that contains a graphical editor, customizable block libraries, and solvers for multidomain simulation and model-based design in MATLAB. It supports simulation, automatic code generation, and continuous test and verification of embedded systems. | matlab, block diagram, multidomain simulation, simulation software, model based design, automatic code generation | is listed by: SoftCite | Commercially available, Free trial available | SCR_014744 | 2026-09-12 12:58:21 | 396 | ||||||||||
|
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 | 2026-09-12 12:58:22 | 27 | |||||||||||
|
Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | 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 | 2026-09-12 12:58:20 | 1993 | |||||
|
WinWCP Resource Report Resource Website 100+ mentions |
WinWCP (RRID:SCR_014713) | data acquisition software, data analysis software, data processing software, software application, 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 | 2026-09-12 12:58:21 | 435 | |||||||||
|
PAUP Resource Report Resource Website 1000+ mentions |
PAUP (RRID:SCR_014931) | PAUP | data analysis software, data processing software, data visualization software, software application, software resource | 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 | 2026-09-12 12:58:23 | 2292 | |||||||
|
Nexus Resource Report Resource Website 100+ mentions |
Nexus (RRID:SCR_015001) | data acquisition software, data processing software, software application, software resource | Data capture software for use with Vicon motion capture system. Its features include MATLAB integration, Python pre-installed, customized workflow, and automated quality assessment. | biomechanics, motion capture |
is listed by: SoftCite works with: MATLAB works with: Bodybuilder |
Available for download | https://www.vicon.com/downloads/core-software/nexus | SCR_015001 | Nexus 2, Nexus 1.8.5, Nexus 2.5.0, Nexus 2.4.0 | 2026-09-12 12:58:24 | 397 | ||||||||
|
Ringo Resource Report Resource Website 10+ mentions |
Ringo (RRID:SCR_012973) | Ringo | software resource | Software package that facilitates the primary analysis of ChIP-chip data. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00809 | SCR_012973 | 2026-09-12 12:57:56 | 38 | ||||||||||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | data analysis software, data processing software, software application, software resource | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs, https://sources.debian.org/src/macs/ | SCR_013291 | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-09-12 12:58:01 | 1418 |
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