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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GenePattern Resource Report Resource Website 1000+ mentions |
GenePattern (RRID:SCR_003201) | GenePattern | data analysis software, data processing software, software application, software resource | A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. | gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is affiliated with: GenePattern Notebook is related to: TIGRESS has parent organization: Broad Institute |
NCI ; NIGMS |
PMID:16642009 | Free, Freely available | biotools:genepattern, OMICS_01855, nif-0000-30654 | https://bio.tools/genepattern | SCR_003201 | 2026-08-29 11:21:46 | 1135 | |||||
|
RevMan Resource Report Resource Website 10000+ mentions |
RevMan (RRID:SCR_003581) | RevMan | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00244 | SCR_003581 | Review Manager | 2026-08-29 11:21:58 | 12962 | ||||||||
|
MODELLER Resource Report Resource Website 5000+ mentions |
MODELLER (RRID:SCR_008395) | data or information resource, portal, simulation software, software application, software resource, topical portal | Software tool as Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Used for homology or comparative modeling of protein three dimensional structures. User provides alignment of sequence to be modeled with known related structures and MODELLER automatically calculates model containing all non hydrogen atoms. | comparative, protein, structure, modelling, satisfaction, spatial, restrain, homology, 3D, alignment, sequence, hydrogen, atom, cluster |
is listed by: SoftCite has parent organization: University of California at San Francisco; California; USA |
IBM ; Intel ; NIGMS P01 GM71790; NIGMS R01 GM54762; NIGMS U54 GM62529; NIH P01 A135707; Sandler Family Supporting Foundation |
Restricted | nif-0000-30054 | SCR_008395 | 2026-08-29 11:23:14 | 5873 | ||||||||
|
FigTree Resource Report Resource Website 10000+ mentions |
FigTree (RRID:SCR_008515) | data processing software, data visualization software, software application, software resource | A graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST. | data visualization software, graphical viewer, phylogenetic tree, annotate |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Edinburgh; Scotland; United Kingdom |
OMICS_04268, nif-0000-30567 | https://sources.debian.org/src/figtree/ | SCR_008515 | FigTree | 2026-08-29 11:23:31 | 12345 | ||||||||
|
Augustus Resource Report Resource Website 1000+ mentions |
Augustus (RRID:SCR_008417) | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes. | software, gene, prediction, eucaryotic, genomic, sequence |
is used by: BRAKER is used by: BRO_annotation is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: Gsnap2Augustus |
Deutsche Forschungsgemeinschaft (DFG) HO4545/1-1;; STA1009/6-1 ; Institute for Mathematics and Computer Science ; Ernst Moritz Arndt University of Greifswald |
PMID:23700307 DOI:10.1093/bioinformatics/btw494 |
Free, Available for download, Freely available | SCR_015981, OMICS_07777, nif-0000-30133 | https://sources.debian.org/src/autodock-vina/ | SCR_008417 | Augustus: Gene Prediction, WebAUGUSTUS, Augustus, Augustus [gene prediction] | 2026-08-29 11:23:30 | 3886 | |||||
|
Research Randomizer Resource Report Resource Website 1000+ mentions |
Research Randomizer (RRID:SCR_008563) | data access protocol, software resource, web service | This site is designed for researchers and students who want a quick way to generate random numbers or assign participants to experimental conditions. Research Randomizer can be used in a wide variety of situations, including psychology experiments, medical trials, and survey research. The program uses a JavaScript random number generator to produce customized sets of random numbers. Since its release in 1997, Research Randomizer has been used to generate number sets over 10.7 million times. This service is part of Social Psychology Network and is fast, free, and runs with any recent web browser as long as JavaScript isn''t disabled. Research Randomizer is a free service offered to students and researchers interested in conducting random assignment and random sampling. By using this service, you agree to abide by the SPN User Policy and to hold Research Randomizer and its staff harmless in the event that you experience a problem with the program or its results. Although every effort has been made to develop a useful means of generating random numbers, Research Randomizer and its staff do not guarantee the quality or randomness of numbers generated. Any use to which these numbers are put remains the sole responsibility of the user who generated them. What are the system requirements needed to run Research Randomizer? This program works best with Firefox and other recent web browsers. If you''re using a browser that came with America Online, or older browsers made prior to 2003, you may experience some difficulties with Research Randomizer. You may also not be able to use Research Randomizer with some limited-function browsers that do not fully support JavaScript, such as the Opera broswer used on certain game consoles. We would suggest that you update to a fairly recent, fully- functional stand-alone browser. How do I know what browser I am using? The easiest way to find this out is to click Help on the pulldown menu at the top of the screen. One of the options should be About Mozilla Firefox, About Internet Explorer, About Netscape, or something similar. Selecting this option will open a window that displays the name, version number, and copyright date of your browser. How does Research Randomizer generate its numbers? Research Randomizer uses the Math.random method within the JavaScript programming language to generate its random numbers for all modern web browsers. If you are using an older version of Microsoft Internet Explorer or Netscape Navigator (that is prior to version 4.0 of either), Research Randomizer uses an adaptation of the Central Randomizer by Paul Houle. Note that Research Randomizer no longer supports much-older browsers by other vendors (e.g., Mosaic). Who designed Research Randomizer? The original idea and programming for Research Randomizer came from Geoffrey C. Urbaniak in 1997. Research Randomizer was then jointly developed with Scott Plous, webmaster of Social Psychology Network, and online tutorials were added to the main program. In 1999 the site was redesigned with the assistance of Mike Lestik, in 2003 Mike Lestik added the download function, and in 2007 Mike Lestik and Scott Plous redesigned the site and added new content. | is listed by: SoftCite | nif-0000-31448 | SCR_008563 | Research Randomizer | 2026-08-29 11:23:19 | 3018 | ||||||||||
|
Scion Image Resource Report Resource Website 5000+ mentions |
Scion Image (RRID:SCR_008673) | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Commercial software vendor. | imaging, industrial, scientific | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33408 | SCR_008673 | 2026-08-29 11:23:22 | 5759 | |||||||||
|
MACH Resource Report Resource Website 500+ mentions |
MACH (RRID:SCR_009621) | data analysis software, data processing software, software application, software resource | QTL analysis based on imputed dosages/posterior_probabilities. | genetic association, genomic analysis, imaging genomics, snp, gene, quantitative trait analysis, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 DOI:10.1002/gepi.20533 |
Free, Non-commercial, Acknowledgement requested | nlx_155856, biotools:mach | http://www.nitrc.org/projects/mach, https://bio.tools/mach | https://sources.debian.org/src/mach-haplotyper/ | SCR_009621 | mach2qtl, MaCH | 2026-08-29 11:23:36 | 937 | |||||
|
Image Pro Plus Resource Report Resource Website 10000+ mentions |
Image Pro Plus (RRID:SCR_007369) | data acquisition software, data processing software, image acquisition software, image analysis software, software application, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software package to capture, process, measure, analyze and share images and data. | morphometric, image analysis, image acquisition, automation, classification, microscope control | is listed by: SoftCite | nif-0000-00313, SCR_015803, SCR_016879 | SCR_007369 | Image-Pro Plus, Image-Pro Plus Morphometric Analysis Software | 2026-08-29 11:22:51 | 18774 | |||||||||
|
UCHIME Resource Report Resource Website 1000+ mentions |
UCHIME (RRID:SCR_008057) | UCHIME | software resource | An algorithm for detecting chimeric sequences. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_01115 | SCR_008057 | 2026-08-29 11:23:07 | 1927 | ||||||||||
|
QIIME Resource Report Resource Website 10000+ mentions |
QIIME (RRID:SCR_008249) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics. | microbiome, microbial community, sequence data, data analysis software, bio.tools |
is used by: SortMeRNA is used by: Nephele is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Colorado Boulder; Colorado; USA |
DOI:10.1038/nmeth.f.303 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01118, SCR_011948, OMICS_01521, biotools:qiime | https://bio.tools/qiime | SCR_008249 | Quantitative Insights Into Microbial Ecology | 2026-08-29 11:23:10 | 11177 | ||||||
|
BEDTools Resource Report Resource Website 10000+ mentions |
BEDTools (RRID:SCR_006646) | BEDTools | software resource | A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line. | genomics, bed, sam, bam, overlap, sequencing, intersect, coverage, gff, vcf, bedgraph, interval, genome arithmetic, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Hydra is related to: pybedtools is required by: SL-quant |
PMID:20110278 DOI:10.1093/bioinformatics/btq033 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01159, biotools:bedtools | https://code.google.com/p/bedtools/, https://bio.tools/bedtools, https://sources.debian.org/src/bedtools/ | SCR_006646 | bedtools - a swiss army knife for genome arithmetic, bedtools: a flexible suite of utilities for comparing genomic features | 2026-08-29 11:22:46 | 11365 | |||||
|
geNORM Resource Report Resource Website 5000+ mentions |
geNORM (RRID:SCR_006763) | GENORM | data analysis software, data processing software, software application, software resource | Software to determine most stable reference (housekeeping) genes from set of tested candidate reference genes in given sample panel. From this, gene expression normalization factor can be calculated for each sample based geometric mean of user-defined number of reference genes. | reference gene, quantitative real time pcr |
is used by: RefFinder is listed by: OMICtools is listed by: SoftCite is related to: qBasePLUS has parent organization: Ghent University; Ghent; Belgium |
PMID:19131113 PMID:12519963 |
nlx_156922, OMICS_02316 | http://medgen.ugent.be/~jvdesomp/genorm/ | SCR_006763 | 2026-08-29 11:22:50 | 5414 | |||||||
|
ShortRead Resource Report Resource Website 100+ mentions |
ShortRead (RRID:SCR_006813) | ShortRead | software resource | Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats. | high throughput sequence data, short read, DNA sequences, short read data |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: Bioconductor |
PMID:19654119 | Free, Available for download, Freely available | OMICS_01076 | https://sources.debian.org/src/r-bioc-shortread/ | SCR_006813 | ShortRead - Classes and methods for high-throughput short-read sequencing data. | 2026-08-29 11:22:52 | 235 | |||||
|
I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | data analysis software, data processing software, software application, software resource | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-08-29 11:24:50 | 3874 | |||||
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Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality. | transcriptome, rna-seq, rna seq, cuffmerge, cufflink, cuffcompare, transfrags, artifacts, gtf file, transcriptome assembly, expression analysis, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite works with: GeneScissors is hosted by: GitHub |
DOI:10.1038/nbt.1621 | Acknowledgement requested, Source code available on GitHub | biotools:cufflinks, OMICS_01304, SCR_013307 | https://github.com/cole-trapnell-lab/cufflinks, https://bio.tools/cufflinks, https://sources.debian.org/src/cufflinks/ | SCR_014597 | 2026-08-29 11:24:49 | 9083 | |||||||
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Minitab Resource Report Resource Website 5000+ mentions |
Minitab (RRID:SCR_014483) | data analysis software, data processing software, software application, software resource | A statistical software package that allows the user to import data, create graphs, and perform statistical analysis. It can perform basic statistical tests like descriptive statistics, hypothesis tests, confidence intervals, and normality tests as well as regression and ANOVA and quality assessment. | data analysis, statistical analysis, hypothesis, confidence, descriptive | is listed by: SoftCite | SCR_014483 | 2026-08-29 11:24:49 | 6109 | |||||||||||
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COMSOL Multiphysics Resource Report Resource Website 50+ mentions |
COMSOL Multiphysics (RRID:SCR_014767) | simulation software, software application, software resource | General-purpose software platform for modeling and simulating physics-based problems which accounts for coupled or multiphysics phenomena. The platform includes a set of core physics interfaces for common physics application areas such as structural analysis, laminar flow, pressure acoustics, transport of diluted species, electrostatics, electric currents, heat transfer, and Joule heating. | simulation software, software platform, physics, problem solver | is listed by: SoftCite | Commercially available | SCR_014767 | 2026-08-29 11:24:53 | 51 | ||||||||||
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CVODE Resource Report Resource Website 50+ mentions |
CVODE (RRID:SCR_014696) | data analysis software, data processing software, software application, software resource | Solver for stiff and nonstiff ordinary differential equation (ODE) systems (initial value problem), given in explicit form y' = f(t,y), based on Adams and BDF methods. It is one of the programs that makes up the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis software, solver, equation solver, ordinary differential equation, differential equation, stiff, nonstiff | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014696 | SUNDIALS CVODE | 2026-08-29 11:24:51 | 56 | |||||||||
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MedCalc Resource Report Resource Website 10000+ mentions |
MedCalc (RRID:SCR_015044) | data analysis software, data processing software, software application, software resource | Statistical software for ROC curve analysis. MedCalc performs several statistical tests such as method comparison, method evaluation, reference intervals, and meta-analysis. | statistic, statistical analysis, roc curve, reference software | is listed by: SoftCite | Commercially available, Available for purchase, Trial available | SCR_015044 | 2026-08-29 11:25:08 | 19712 |
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