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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Design-Expert Resource Report Resource Website 10+ mentions |
Design-Expert (RRID:SCR_022671) | software application, software resource, data analytics software | Statistical software package from Stat-Ease Inc. to perform design of experiments. Offers comparative tests, screening, characterization, optimization, robust parameter design, mixture designs and combined designs. | Stat-Ease Inc., experiments design, comparative tests, screening, characterization, optimization, parameter design, mixture designs, combined designs | is listed by: SoftCite | Restricted | SCR_022671 | 2026-08-04 09:45:04 | 41 | ||||||||||
|
Treerecs Resource Report Resource Website 1+ mentions |
Treerecs (RRID:SCR_024497) | software application, software resource | Open source, species and gene tree reconciliation software. Software integrated phylogenetic tool, from sequences to reconciliations. Used to correct, rearrange and reroot gene trees with regard to given species tree. | species and gene tree reconciliation, integrated phylogenetic, from sequences to reconciliations, correct gene trees, rearrange gene trees, reroot gene trees, | is listed by: SoftCite | PMID:33085745 | Free, Available for download, Freely available | https://project.inria.fr/treerecs/ | SCR_024497 | 2026-08-04 09:45:32 | 1 | ||||||||
|
Evalue Resource Report Resource Website 10+ mentions |
Evalue (RRID:SCR_024506) | web application, software resource, source code | Web application as E-value calculator that compute E-values for variety of outcome measures, including risk ratios, odds ratios, rate ratios, risk differences, hazard ratios, and standardized mean differences. | E-value calculator, compute E-values for variety of outcome measures, | is listed by: SoftCite | PMID:29912013 | Free, Available for download, Freely available | https://github.com/mayamathur/evalue_package | SCR_024506 | 2026-08-04 09:45:32 | 14 | ||||||||
|
Ensembl Genome Browser Resource Report Resource Website 1000+ mentions |
Ensembl Genome Browser (RRID:SCR_013367) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17,2022. Genome databases for vertebrates and other eukaryotic species. Analysis and annotation maintained on current data.Distribution of analysis to other bioinformatics laboratories. Ensembl concentrates on vertebrate genomes, but other groups have adapted system for use with plant and fungal genomes (see Powered by Ensembl list on website). |
is listed by: SoftCite has parent organization: Ensembl |
European Bioinformatics Institute ; Wellcome Trust Sanger Institute |
THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-30518 | http://uswest.ensembl.org/index.html | SCR_013367 | 2026-08-04 09:43:11 | 1179 | ||||||||
|
Web of Science Resource Report Resource Website 10+ mentions |
Web of Science (RRID:SCR_022706) | database, data or information resource | Database of bibliographic citations of multidisciplinary areas that covers various journals of medical, scientific, and social sciences including humanities.Publisher independent global citation database. | Clarivate, publisher independent, global citation database, bibliographic citations of multidisciplinary areas, various journals | is listed by: SoftCite | Free | SCR_022706 | Web of Knowledge | 2026-08-04 09:45:05 | 18 | |||||||||
|
CASAVA Resource Report Resource Website 1000+ mentions |
CASAVA (RRID:SCR_001802) | CASAVA | software application, software resource | Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting | gene, genetic, genomic, linux |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite |
Free, Available for download, Freely available | nlx_154257, OMICS_01123 | http://www.illumina.com/software/genome_analyzer_software.ilmn | SCR_001802 | Consensus Assessment of Sequence And VAriation | 2026-08-04 09:40:28 | 1899 | ||||||
|
Statistical Analysis System Resource Report Resource Website 5000+ mentions |
Statistical Analysis System (RRID:SCR_008567) | SAS | software application, software resource, data analytics software, data management software | Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS. | Explore, analyze, visualize, data, standardized, management, statistics | is listed by: SoftCite | Restircted | nif-0000-31484 | https://www.sas.com/en_us/software/platform.html, https://www.sas.com/en_us/software/sas9.html | SCR_008567 | Statistical Analysis System, SAS Intelligence Platform, SAS 9.3, SAS 9.4 | 2026-08-04 09:42:09 | 7165 | ||||||
|
SciPy Resource Report Resource Website 10000+ mentions |
SciPy (RRID:SCR_008058) | software application, software resource | A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console. | python, software, open source |
uses: Python Programming Language is used by: PyDSTool is used by: Elephant is used by: Stimfit is used by: Sklearn is listed by: SoftCite is related to: IPython is related to: NumPy is related to: IPython Notebook is related to: MNE software is related to: DE-Sim is required by: TomoMiner is required by: Short Read Sequence Typing for Bacterial Pathogens |
Public, Free | nif-0000-10422 | SCR_008058 | SciPy, Scientific Tools for Python | 2026-08-04 09:42:05 | 12935 | ||||||||
|
Blender Resource Report Resource Website 1000+ mentions |
Blender (RRID:SCR_008606) | database, data or information resource | Blender is the free open source 3D content creation suite, available for all major operating systems under the GNU General Public License. Because of the overwhelming success of the first open movie project, Ton Roosendaal, the Blender Foundation''s chairman, has established the Blender Institute. This now is the permanent office and studio to more efficiently organize the Blender Foundation goals, but especially to coordinate and facilitate Open Projects related to 3D movies, games or visual effects. | FASEB list |
is listed by: SoftCite is related to: NeuroMorph |
nif-0000-31943 | SCR_008606 | Blender | 2026-08-04 09:42:11 | 2220 | |||||||||
|
Google Scholar Resource Report Resource Website 10000+ mentions |
Google Scholar (RRID:SCR_008878) | Google Scholar | database, data or information resource | Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. Google Scholar helps you find relevant work across the world of scholarly research. Features of Google Scholar * Search diverse sources from one convenient place * Find articles, theses, books, abstracts or court opinions * Locate the complete document through your library or on the web * Learn about key scholarly literature in any area of research How are documents ranked? Google Scholar aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature. * Publishers - Include your publications in Google Scholar * Librarians - Help patrons discover your library''s resources | literature |
is used by: Writefull is listed by: SoftCite is parent organization of: Google Scholar Blog |
nlx_151304 | SCR_008878 | 2026-08-04 09:42:14 | 38796 | |||||||||
|
T-Coffee Resource Report Resource Website 1000+ mentions |
T-Coffee (RRID:SCR_011818) | T-Coffee | data analysis service, analysis service resource, production service resource, service resource | A multiple sequence alignment server which can align Protein, DNA and RNA sequences. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:10964570 DOI:10.1006/jmbi.2000.4042 |
biotools:tcoffee, OMICS_00989 | https://bio.tools/tcoffee, https://sources.debian.org/src/t-coffee/ | SCR_011818 | T-Coffee: Aligns DNA RNA or Proteins using the default T-Coffee | 2026-08-04 09:42:51 | 1121 | ||||||
|
ProbCons Resource Report Resource Website 100+ mentions |
ProbCons (RRID:SCR_011813) | ProbCons | data analysis service, analysis service resource, production service resource, service resource | Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Stanford University; Stanford; California |
PMID:15687296 DOI:10.1101/gr.2821705 |
OMICS_00986, biotools:probcons | https://bio.tools/probcons, https://sources.debian.org/src/probcons/ | SCR_011813 | ProbCons: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences | 2026-08-04 09:42:51 | 106 | ||||||
|
GeneVenn Resource Report Resource Website 100+ mentions |
GeneVenn (RRID:SCR_012117) | data analysis service, analysis service resource, production service resource, service resource | A web application creating Venn diagrams from two or three gene lists. | web app |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:17597932 | OMICS_05568 | SCR_012117 | 2026-08-04 09:42:54 | 101 | |||||||||
|
TBLASTN Resource Report Resource Website 5000+ mentions |
TBLASTN (RRID:SCR_011822) | TBLASTN | data analysis service, analysis service resource, production service resource, service resource | Tool to search translated nucleotide databases using a protein query. | protein |
is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI |
OMICS_00999 | SCR_011822 | Translated BLAST: tblastn | 2026-08-04 09:42:51 | 5523 | ||||||||
|
FGENESH Resource Report Resource Website 100+ mentions |
FGENESH (RRID:SCR_011928) | FGENESH | data analysis service, analysis service resource, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fgenesh, OMICS_01483 | https://bio.tools/fgenesh | SCR_011928 | 2026-08-04 09:42:52 | 330 | |||||||
|
BaCelLo Resource Report Resource Website 10+ mentions |
BaCelLo (RRID:SCR_011965) | BaCelLo | data analysis service, analysis service resource, production service resource, service resource | A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable. | protein, data set, proteome |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bologna; Bologna; Italy |
PMID:16873501 | OMICS_01616 | SCR_011965 | 2026-08-04 09:42:53 | 45 |
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