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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RepeatModeler Resource Report Resource Website 1000+ mentions |
RepeatModeler (RRID:SCR_015027) | data analysis software, data processing software, sequence analysis software, software application, software resource | Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence analysis, sequence repeats, repeat identification, bio.tools |
uses: RepeatScout is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Dfam |
Institute for Systems Biology ; NHGRI R44 HG02244; NHGRI R01 HG002939 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:repeatmodeler | https://bio.tools/repeatmodeler | SCR_015027 | 2026-09-05 06:30:06 | 3249 | |||||||
|
CMap Resource Report Resource Website 500+ mentions |
CMap (RRID:SCR_016204) | data or information resource, data set, database, software resource, web application | 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 | 2026-09-05 06:30:07 | 789 | |||||||
|
pheatmap Resource Report Resource Website 1000+ mentions |
pheatmap (RRID:SCR_016418) | pheatmap | data acquisition software, data processing software, image acquisition software, software application, software resource, software toolkit | Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters. | draw, clustered, heatmap, control, graphical, parameter, size, shape, text, bio.tools |
is used by: ClustVis is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | biotools:pheatmap, OMICS_26726 | https://github.com/raivokolde/pheatmap, https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf, https://bio.tools/pheatmap, https://sources.debian.org/src/r-cran-pheatmap/ | SCR_016418 | pretty heatmap | 2026-09-05 06:30:07 | 1249 | ||||||
|
Protein preparation Wizard Resource Report Resource Website 10+ mentions |
Protein preparation Wizard (RRID:SCR_016749) | simulation software, software application, software resource | Software tool for correcting common structural problems and creating reliable, all atom protein models. | correcting, structural, problem, atom, protein, model, virtual, docking, method |
is listed by: SoftCite has parent organization: Schrodinger |
Commercially available, Training available | SCR_016749 | protein preparation wizard, Protein Preparation Wizard | 2026-09-05 06:30:08 | 13 | |||||||||
|
OpenEpi Resource Report Resource Website 100+ mentions |
OpenEpi (RRID:SCR_021913) | data analytics software, software application, software resource, software toolkit | Web based, open source, operating system independent series of programs designed for use in public health and medicine for training or practice that provide number of epidemiologic and statistical tools for summary data. Developed in JavaScript and HTML, and can be run in modern web browsers. Program can be run from OpenEpi website or downloaded and run without web connection. | epidemiologic tool, statistical tool, epidemiologic statistics, public health |
is listed by: SoftCite has parent organization: Emory University; Georgia; USA |
Bill and Melinda Gates Foundation | PMID:19445426 | Free, Available for download, Freely available | SCR_021913 | 2026-09-05 06:30:11 | 160 | ||||||||
|
Epik Resource Report Resource Website 1+ mentions |
Epik (RRID:SCR_016745) | simulation software, software application, software resource | Software program for pKa prediction and protonation state generation for drug like molecules. | predict, pKa, value, chemical, structure, drug, profile, protonation, state, molecule, Schrodinger |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger |
PMID:17899391 | Commercially available | SCR_016745 | 2026-09-05 06:28:13 | 6 | |||||||||
|
Ligprep Resource Report Resource Website 50+ mentions |
Ligprep (RRID:SCR_016746) | Ligprep | simulation software, software application, software resource | Software tool to correct and optimize the ligands by generating different protonation states, stereochemistry, tautomers, and ring conformations. Used to generate accurate, energy minimized 3D molecular structures. | correct, optimize, ligand, protonation, stereochemistry, tautomer, conformation, energy, minimized, 3D, moleular, structure |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger works with: Glide works with: Phase |
Commercially available | SCR_016746 | LigPrep, LigandPreparation, Ligand preparation | 2026-09-05 06:28:13 | 50 | ||||||||
|
NetworkX Resource Report Resource Website 100+ mentions |
NetworkX (RRID:SCR_016864) | data analysis software, data processing software, network analysis software, software application, software resource | Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | create, analysis, structure, dynamic, function, complex, network, data | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/networkx/networkx | SCR_016864 | 2026-09-05 06:28:14 | 132 | |||||||||
|
ProSAS Resource Report Resource Website 1+ mentions |
ProSAS (RRID:SCR_007876) | ProSAS | data or information resource, database | This database provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. ProSAS comprehensively annotates protein structures for several Ensembl genomes and alternative transcripts can be analyzed on the protein structure and protein function level using the intuitive user interface of the database. Users can search based on Ensembl gene or Ensembl transcript ids, Gene descriptions, Uniprot gene names, Genes matching patterns, Swissprot/Uniprot identifiers or Affymetrix probeset ids. |
is listed by: SoftCite has parent organization: Ludwig-Maximilians-University; Munich; Germany |
SCR_007876 | Protein Structure and Alternative Splicing | 2026-09-05 06:31:47 | 1 | ||||||||||
|
Blender Resource Report Resource Website 1000+ mentions |
Blender (RRID:SCR_008606) | data or information resource, database | 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 | 2026-09-05 06:31:53 | 2546 | |||||||||
|
Google Scholar Resource Report Resource Website 10000+ mentions |
Google Scholar (RRID:SCR_008878) | Google Scholar | data or information resource, database | 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 | 2026-09-05 06:31:55 | 43739 | |||||||||
|
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 | 2026-09-05 06:33:18 | 1 | ||||||||
|
Evalue Resource Report Resource Website 10+ mentions |
Evalue (RRID:SCR_024506) | software resource, source code, web application | 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 | 2026-09-05 06:33:18 | 24 | ||||||||
|
qBasePLUS Resource Report Resource Website 100+ mentions |
qBasePLUS (RRID:SCR_003370) | qbase+ | commercial organization, software resource | Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology. | real-time quantitative pcr |
is listed by: OMICtools is listed by: SoftCite is related to: geNORM has parent organization: Biogazelle |
PMID:17291332 | Free, Available for download, Freely available | OMICS_02320 | https://biogazelle-qbaseplus.software.informer.com/2.0/ | http://medgen.ugent.be/qbase/ | SCR_003370 | 2026-09-05 06:33:24 | 344 | |||||
|
Picard Resource Report Resource Website 10000+ mentions Rating or validation data |
Picard (RRID:SCR_006525) | software resource, software toolkit, source code | Java toolset for working with next generation sequencing data in the BAM format. | next generation sequencing, java, bam |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge has parent organization: Broad Institute is required by: SL-quant |
Available for download, Free | OMICS_01066 | http://sourceforge.net/projects/picard/, https://github.com/broadinstitute/picard, https://sources.debian.org/src/picard-tools/ | SCR_006525 | 2026-09-05 06:33:27 | 15653 | ||||||||
|
SAM Resource Report Resource Website 100+ mentions |
SAM (RRID:SCR_010951) | software resource | Software for genomic expression data mining using a statistical technique for finding significant genes in a set of microarray experiments. | genomic expression, data mining, finding significant genes, microarray experiments, |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: pysam has parent organization: Stanford University; Stanford; California |
Commercial use requires license, Registration required | OMICS_01314, OMICS_00779, SCR_011888 | https://sources.debian.org/src/r-cran-samr/ | SCR_010951 | SAM: Significance Analysis of Microarrays, Significance Analysis of Microarrays | 2026-09-05 06:33:44 | 235 | |||||||
|
SABmark Resource Report Resource Website 1+ mentions |
SABmark (RRID:SCR_011817) | SABmark | data or information resource, data set | Downloadable data set designed to assess the performance of both multiple and pairwise (protein) sequence alignment algorithms, and is extremely easy to use. Currently, the database contains 2 sets, each consisting of a number of subsets with related sequences. It''s main features are: * Covers the entire known fold space (SCOP classification), with subsets provided by the ASTRAL compendium * All structures have high quality, with 100% resolved residues * Structure alignments have been derived carefully, using both SOFI and CE, and Relaxed Transitive Alignment * At most 25 sequences in each subset to avoid overrepresentation of large folds* Automated running, archiving and scoring of programs through a few Perl scripts The Twilight Zone set is divided into sequence groups that each represent a SCOP fold. All sequences within a group share a pairwise Blast e-value of at least 1, for a theoretical database size of 100 million residues. Sequence similarity is thus very low, between 0-25% identity, and a (traceable) common evolutionary origin cannot be established between most pairs even though their structures are (distantly) similar. This set therefore represents the worst case scenario for sequence alignment, which unfortunately is also the most frequent one, as most related sequences share less than 25% identity. The Superfamilies set consists of groups that each represent a SCOP superfamily, and therefore contain sequences with a (putative) common evolutionary origin. However, they share at most 50% identity, which is still challenging for any sequence alignment algorithm. Frequently, alignments are performed to establish whether or not sequences are related. To benchmark this, a second version of both the Twilight Zone and the Superfamilies set is provided, in which to each alignment problem a number of false positives, i.e. sequences not related to the original set, are added. Database specifications: * Current version: 1.65 (concurrent with PDB, SCOP and ASTRAL) * Twilight Zone set (with false positives): 209 groups, 1740 (3280) sequences, 10667 (44056) related pairs * Superfamilies set (with false positives): 425 groups, 3280 (6526) sequences, 19092 (79095) related pairs |
is listed by: OMICtools is listed by: SoftCite has parent organization: Vrije Universiteit Brussel; Brussels; Belgium |
PMID:15333456 | OMICS_00988 | SCR_011817 | SABmark - Sequence and structure Alignment Benchmark, Sequence Alignment Benchmark, Sequence and structure Alignment Benchmark | 2026-09-05 06:33:50 | 8 | ||||||||
|
Stata Resource Report Resource Website 10000+ mentions |
Stata (RRID:SCR_012763) | software application, software resource | Software package for statistical analysis and presentation of graphics. Statistical software for data science. | statistical analysis, presentation of graphics, data science, | is listed by: SoftCite | Restricted | nlx_156918 | SCR_012763 | 2026-09-05 06:33:58 | 49366 | |||||||||
|
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 | 2026-09-05 06:32:25 | 1960 | ||||||
|
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 | 2026-09-05 06:32:39 | 16188 |
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