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https://github.com/uclinfectionimmunity/Decombinator
Software suite for analysis of T cell receptor repertoire data. Used for fast, efficient analysis of T cell receptor (TcR) repertoire samples, designed to be accessible to those with no previous programming experience.
Proper citation: Decombinator (RRID:SCR_006732) Copy
http://dgidb.genome.wustl.edu/
A database of drug-gene relationships that provides drug-gene interactions and potential druggability data given list of genes. There are about 15 data sources that are being aggregated by DGIdb, with update date and these data sources are listed on this page: http://dgidb.genome.wustl.edu/sources, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: DGIdb (RRID:SCR_006608) Copy
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
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
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
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
Web based integrative platform for transcriptional regulation studies.
Proper citation: Cistrome (RRID:SCR_000242) Copy
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
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
Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data.
Proper citation: Dipy (RRID:SCR_000029) Copy
A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures.
Proper citation: PyMOL (RRID:SCR_000305) Copy
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
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
https://www.openmicroscopy.org/site/products/bio-formats
Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard.
Proper citation: Bio-Formats (RRID:SCR_000450) Copy
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
An open mark-up language for NMR data.
Proper citation: nmrML (RRID:SCR_000467) Copy
https://github.com/PacificBiosciences/pbcore
Software Python library for reading and writing PacBio data files.
Proper citation: pbcore (RRID:SCR_000454) Copy
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
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
http://neuralensemble.org/trac/OpenElectrophy
Software Python module for electrophysiology data analysis.
Proper citation: OpenElectrophy (RRID:SCR_000819) Copy
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