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http://www.pseudomonas.com/

Database of peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome expanded to include all Pseudomonas species to facilitate cross-strain and cross-species genome comparisons with high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. The current annotation is updated using recent research literature and peer-reviewed submissions by a worldwide community of PseudoCAP (Pseudomonas aeruginosa Community Annotation Project) participating researchers. If you are interested in participating, you are invited to get involved. Many annotations, DNA sequences, Orthologs, Intergenic DNA, and Protein sequences are available for download.

Proper citation: Pseudomonas Genome Database (RRID:SCR_006590) Copy   

•   Source: SciCrunch Registry

http://bar.utoronto.ca/welcome.htm

Web-based tools for working with functional genomics and other data, including Gene Expression and Protein Tools, Molecular Markers and Mapping Tools, and Other Genomic Tools. Most are designed with the plant (mainly Arabidopsis) researcher in mind, but a couple of them can be useful to the wider research community, e.g. Mouse eFP Browser or BlastDigester. The associated paper for most tools is available.

Proper citation: BAR (RRID:SCR_006748) Copy   

•   Source: SciCrunch Registry

http://www.maizegdb.org

Collection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images.

Proper citation: MaizeGDB (RRID:SCR_006600) Copy   

•   Source: SciCrunch Registry

http://www.proteinatlas.org/

Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.

Proper citation: The Human Protein Atlas (RRID:SCR_006710) Copy   

•   Source: SciCrunch Registry

http://cistrome.org

Web based integrative platform for transcriptional regulation studies.

Proper citation: Cistrome (RRID:SCR_000242) Copy   

•   Source: SciCrunch Registry

http://docking.sce.ntu.edu.sg/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor.

Proper citation: CovalentDock Cloud (RRID:SCR_000126) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/cn.farms.html

Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff.

Proper citation: cn.FARMS (RRID:SCR_000289) Copy   

•   Source: SciCrunch Registry

http://www.ngsbicocca.org/html/fusion_analyser.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data.

Proper citation: Fusion Analyser (RRID:SCR_000059) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.

Proper citation: CorMut (RRID:SCR_000053) Copy   

•   Source: SciCrunch Registry

http://www.cs.toronto.edu/~hilal/rnacontext/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Motif finding software suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RNA-binding proteins (RBPs) for a wide range of RNA sequences and structures. The tool is also implemented in a website.

Proper citation: RNAcontext (RRID:SCR_000179) Copy   

•   Source: SciCrunch Registry

http://nmrml.org/

An open mark-up language for NMR data.

Proper citation: nmrML (RRID:SCR_000467) Copy   

•   Source: SciCrunch Registry

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

Software for adaptive Gene Picking for Microarray Expression Data Analysis.

Proper citation: pickgene (RRID:SCR_001331) Copy   

•   Source: SciCrunch Registry

https://vcftools.github.io/index.html

Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API.

Proper citation: VCFtools (RRID:SCR_001235) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/mckinsel/shortfuse

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2.

Proper citation: ShortFuse (RRID:SCR_001107) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.

Proper citation: metahdep (RRID:SCR_001225) Copy   

•   Source: SciCrunch Registry

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

A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

Proper citation: globaltest (RRID:SCR_001256) Copy   

•   Source: SciCrunch Registry

http://sun.aei.polsl.pl/dsrc/

An application designed for compression of data files containing reads from DNA sequencing in FASTQ format. Its main features include multithreaded compression of FASTQ output, python and C++ libraries, and support for lossy IDs compression.

Proper citation: DSRC (RRID:SCR_001005) Copy   

•   Source: SciCrunch Registry

http://dna.leeds.ac.uk/illuminator/

A sequence alignment program for the output from Illumina GA-II clonal sequencers. It uses an algorithm that indexes the reference sequence as a series of 8-mers and then matches the genomic reads to the 8-mer index, in a mutation-tolerant way permitting identification of single-nucleotide substitutions and indels.

Proper citation: Illuminator (RRID:SCR_001019) Copy   

•   Source: SciCrunch Registry

https://immersive-analytics.infotech.monash.edu/vanted/

Software tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data.

Proper citation: Visualization and Analysis of Networks containing Experimental Data (VANTED) (RRID:SCR_001138) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/services/NetNGlyc-1.0/

Server that predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. NetNGlyc 1.0 is also available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms.

Proper citation: NetNGlyc (RRID:SCR_001570) Copy   

•   Source: SciCrunch Registry