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http://andestools.sourceforge.net/

Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses.

Proper citation: ANDES (RRID:SCR_002791) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/gap

Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits.

Proper citation: NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/pathview.html

A tool set for pathway-based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

Proper citation: Pathview (RRID:SCR_002732) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.charite.de/superpred/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 24,2025. Publicly available web-server to predict medical indication areas based on properties and similarity of chemical compounds. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. The combination of physicochemical property and similarity searching provides the possibility to detect new biologically active compounds and novel targets for drug-like compounds. SuperPred can be applied for drug repositioning purposes, too. A further intention of SuperPred is to find side effects elicited by drugs caused through off-target hits.

Proper citation: SuperPred: Drug classification and target prediction (RRID:SCR_002691) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bio-rainbow/

Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq.

Proper citation: Rainbow (RRID:SCR_002724) Copy   

•   Source: SciCrunch Registry

http://cpc.cbi.pku.edu.cn/

A Support Vector Machine-based classifier to assesses the protein-coding potential of a transcript based on six biologically meaningful sequence features. CPC can discriminate coding from noncoding transcripts with high accuracy and speed. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation. The coding potential calculator tool reads FASTA data format as input.

Proper citation: Coding Potential Calculator (RRID:SCR_002764) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/rBiopaxParser.html

A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported.

Proper citation: rBiopaxParser (RRID:SCR_002744) Copy   

•   Source: SciCrunch Registry

http://www.geneontology.org/

Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.

Proper citation: Gene Ontology (RRID:SCR_002811) Copy   

•   Source: SciCrunch Registry

https://github.com/itojal/hot_scan

A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence.

Proper citation: hot scan (RRID:SCR_002840) Copy   

•   Source: SciCrunch Registry

http://www.greenphyl.org/

A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs.

Proper citation: GreenPhylDB (RRID:SCR_002834) Copy   

•   Source: SciCrunch Registry

http://cgap.nci.nih.gov/

Project to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools

Proper citation: Cancer Genome Anatomy Project (RRID:SCR_003072) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi

A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3.

Proper citation: Primer3Plus (RRID:SCR_003081) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/tweeDEseq.html

Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.

Proper citation: tweeDEseq (RRID:SCR_003038) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/BRAIN.html

Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S).

Proper citation: BRAIN (RRID:SCR_003018) Copy   

•   Source: SciCrunch Registry

http://bibiserv.techfak.uni-bielefeld.de/dialign/

Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/

Proper citation: DIALIGN (RRID:SCR_003041) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bait/

Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

Proper citation: BAIT (RRID:SCR_000511) Copy   

•   Source: SciCrunch Registry

https://github.com/feizhe/PGS

Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures.

Proper citation: PGS (RRID:SCR_000475) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/DOID

Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases.

Proper citation: Human Disease Ontology (RRID:SCR_000476) Copy   

•   Source: SciCrunch Registry

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

Web tool for index free mapping of multiple short reads on a genome.

Proper citation: MPscan (RRID:SCR_000587) Copy   

•   Source: SciCrunch Registry

http://mfuzz.sysbiolab.eu/

Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Mfuzz (RRID:SCR_000523) Copy   

•   Source: SciCrunch Registry