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https://github.com/eduardporta/e-Driver

Software tool to identify cancer driver genes based on linear annotations of biological regions such as protein domains.Uses information on three-dimensional structures of mutated proteins to identify specific structural features. Then algorithm analyzes whether these features are enriched in cancer somatic mutations and are candidate driver genes.

Proper citation: e-Driver (RRID:SCR_002674) Copy   

•   Source: SciCrunch Registry

http://www.vmtk.org/

Software collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

Proper citation: Vascular Modeling Toolkit (RRID:SCR_001893) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/metabnorm/

Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix.

Proper citation: metabnorm (RRID:SCR_001266) Copy   

•   Source: SciCrunch Registry

https://card.mcmaster.ca/

Comprehensive antibiotic resistance database. Bioinformatic database of resistance genes, their products and associated phenotypes.

Proper citation: CARD (RRID:SCR_023995) Copy   

•   Source: SciCrunch Registry

https://cibersort.stanford.edu/

Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.

Proper citation: CIBERSORT (RRID:SCR_016955) Copy   

•   Source: SciCrunch Registry

http://www.atgc-montpellier.fr/phyml/

Web phylogeny server based on the maximum-likelihood principle.

Proper citation: PhyML (RRID:SCR_014629) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/Mash

Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.

Proper citation: Mash (RRID:SCR_019135) Copy   

•   Source: SciCrunch Registry

http://myriads.webs.uvigo.es/

Software package for p value based multiple testing that also implements dependence test and p-value simulation.

Proper citation: Myriads (RRID:SCR_017447) Copy   

•   Source: SciCrunch Registry

http://rloop.bii.a-star.edu.sg/?pg=qmrlfs-finder

A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis.

Proper citation: QmRLFS-finder (RRID:SCR_014584) Copy   

•   Source: SciCrunch Registry

http://www.funrich.org/

A software tool used for functional enrichment and interaction network analysis of genes and proteins. Users can search against a default background database or load customized database. The results can be depicted as venn, bar, column, pie and doughnut charts.

Proper citation: FunRich: Functional Enrichment analysis tool (RRID:SCR_014467) Copy   

•   Source: SciCrunch Registry

http://www.pyrosetta.org/

Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions.

Proper citation: PyRosetta (RRID:SCR_018541) Copy   

•   Source: SciCrunch Registry

https://github.com/AdmiralenOla/Scoary

Software tool that scores components of pan genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes.Designed to take gene presence absence.csv file from Roary as well as traits file created by user and calculate associations between all genes in accessory genome and traits. It reports list of genes sorted by strength of association per trait.

Proper citation: Scoary (RRID:SCR_021087) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.princeton.edu/concavity/

Software for predicting protein ligand binding sites that integrate evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. Used in predicting catalytic sites and drug binding pockets.

Proper citation: Concavity (RRID:SCR_016063) Copy   

•   Source: SciCrunch Registry

https://www.integromics.com/omicsoffice-for-ngs/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.

Proper citation: OmicsOffice for NGS SeqSolve (RRID:SCR_001222) Copy   

•   Source: SciCrunch Registry

http://urgv.evry.inra.fr/CATdb

CATdb collects together all the information on transcriptome experiments done at URGV with CATMA micro arrays. All data in CATdb come from the URGV micro array platforms. Common procedures are used including any steps from the experiment design to the statistical analyses. Directed through a WEB interface, biologists enter the standard description of each experimental step (extraction, labelling, hybridization and scanning). Then, normalization and statistical analyses are done following a set of selected methods depending on the experimental design and array types.

Proper citation: CATdb: a Complete Arabidopsis Transcriptome database (RRID:SCR_007582) Copy   

•   Source: SciCrunch Registry

http://www.allelefrequencies.net

The main purpose of the allelefrequencies.net website is to provide one central source, freely available to all. For the storage of allele frequencies from different polymorphic areas in the HUMAN genome. Users can contribute the results of their work into one common database, and can perform database searches on information already available. They have currently collected data in allele, haplotype and genotype format. The success of this website will depend on you to contribute your data. Sponsors: This resource is supported Royal Liverpool University. Keywords: Allele, Polymorphic, Genome, Database, Data, Haplotype, Genotype,

Proper citation: Allele Frequencies in Worldwide Populations (RRID:SCR_007259) Copy   

•   Source: SciCrunch Registry

http://fullmal.hgc.jp/

Full-Length cDNA Database is a resource for cDNA libraries of arhtropods and parasites. The arthropod species covered are Anopheles stephensi, Glossina morsitans (Tsetse fly), and Dermatophagoides farinae (House dust mite), while the parasitic species included are Plasmodium falciparum (Malaria), Toxoplasma gondii, Cryptosporidium parvum, Babesia bovis (Babesia), and Echinococcus multilocularis. A specialized database of each species is available as a link from the home page. This database has been constructed and maintained since 2001 by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science. Anopheles stephensi, Glossina morsitans, Tsetse fly, Dermatophagoides farinae, House dust mite, Plasmodium falciparum, Malaria, Toxoplasma gondii, Cryptosporidium parvum, Babesia bovis, Babesia, Echinococcus multilocularis, cDNA, cDNA library, arthropod genome, parasite genome

Proper citation: Full-Length cDNA Database (RRID:SCR_007666) Copy   

•   Source: SciCrunch Registry

http://cegg.unige.ch/mirortho

It contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline. The current release of miROrtho covers 46 animal genomes. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline.

Proper citation: miROrtho: the catalogue of animal microRNA genes (RRID:SCR_007797) Copy   

•   Source: SciCrunch Registry

http://biobases.ibch.poznan.pl/ncRNA/

It is intended to provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell. Currently, the database includes over 30,000 individual sequences from 99 species of Bacteria, Archaea and Eukaryota. The primary source of sequences included in the database was the GenBank. Additional annotation information for mouse and human ncRNAs was derived from FANTOM3 database and H-inviational Integrated Database of Annotated Human Genes version 3.4, respectively. Genome mapping information was derived from tha data available at the UCSC Genome Browser site. The sequences and annotations of small cytoplasmic RNAs from bacteria, for which annotation is lacking in the genome sequences, were derived from the Rfam database. The microRNAs or snoRNAs which were available in previous editions, as well as other housekeeping (infrastructural) RNAs (e.g. rRNA, tRNA, snRNA, SRP RNA) are not included in our database to avoid redundancy with more specialized databases which emerged in recent years.

Proper citation: Noncoding RNA database (RRID:SCR_007815) Copy   

•   Source: SciCrunch Registry

http://img.jgi.doe.gov/

Datasets and tools for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context. Plasmids that are not part of a specific microbial genome sequencing project and phage genomes are also included in order to increase its genomic context for comparative analysis. The user interface (see User Interface Map) allows navigating the microbial genome data space along its three key dimensions (genes, genomes, and functions), and groups together the main comparative analysis tools. Microbial genome data analysis in IMG usually starts with the definition of an analysis context in terms of selected genomes, functional annotations, and/or genes, followed by the individual or comparative analysis of genomes, functional annotations, or genes.

Proper citation: IMG (RRID:SCR_007733) Copy   

•   Source: SciCrunch Registry