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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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://sammeth.net/confluence/display/FLUX/Home

Software to recontruct abundances of known transcript forms from RNAseq data. The algorithm works by distributing the reads mapping to a given exonic region (or splice junction) among the transcripts including the exon (or splice junction). The input is the annotation of a reference transcriptome and reads from RNAseq technologies aligned to the genome. From the reference annotation, splicing graphs are produced and reads are mapped to corresponding edges in these graphs according to the position where they align in the genomic sequence. The resulting graph with edges labelled by the number of reads can be interpreted as a flow network where each transcript representing a transportation path from its start to its end and consequently each edge a possibly shared segment of transportation along which a certain number of reads per nucleotide -- i.e., a flux -- is observed. Given a density function of reads along a transcript, the expected participation of each transcript in an edge under consideration can be estimated. The basic idea is to cast back from these latter participations and the observed number of reads - allowing for a certain amount of noise - to the original transcript abundancies. To do so, a linear constraint is formalized for each edge, and an optimal solution for the complete set of constraints is found by a standard linear program solver.

Proper citation: FLUX CAPACITOR (RRID:SCR_006651) 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://www.iqtree.org

Software tool for phylogenomic inference.

Proper citation: IQ TREE (RRID:SCR_021163) Copy   

•   Source: SciCrunch Registry

https://qiime2.org/

Software tool as next generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.Enables researchers to start analysis with raw DNA sequence data and finish with publication quality figures and statistical results. Used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities.

Proper citation: QIIME2 (RRID:SCR_021258) Copy   

•   Source: SciCrunch Registry

https://github.com/amkozlov/raxml-ng

Software phylogenetic tree inference tool which uses maximum likelihood optimality criterion. Used for maximum likelihood phylogenetic inference. Offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML.

Proper citation: RAxML Next Generation (RRID:SCR_022066) Copy   

•   Source: SciCrunch Registry

https://github.com/ekg/vcflib

A C++ library for parsing and manipulating Variant Call Format (VCF) files, and many command-line utilities. The API provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users.

Proper citation: vcflib (RRID:SCR_001231) Copy   

•   Source: SciCrunch Registry

http://crab.rutgers.edu/~dslun/csdeconv/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach.

Proper citation: CSDeconv (RRID:SCR_000016) Copy   

•   Source: SciCrunch Registry

http://www.mattmahoney.net/dc/fastqz/

Source code used to compress FASTQ files. FASTQ is DNA sequencing machine output.

Proper citation: fastqz (RRID:SCR_001006) Copy   

•   Source: SciCrunch Registry

http://hihg.med.miami.edu/software-download/seqem-version-1.0

Online tool for utilizing a genotype calling algorithm for next-generation sequence data.

Proper citation: SeqEM (RRID:SCR_002021) Copy   

•   Source: SciCrunch Registry

https://imagej.net/

Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.

Proper citation: ImageJ (RRID:SCR_003070) Copy   

•   Source: SciCrunch Registry

http://beetlebase.org/

A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded.

Proper citation: BeetleBase (RRID:SCR_001955) Copy   

•   Source: SciCrunch Registry

https://github.com/jts/sga

Software package that functions as a de novo genome assembler based on the concept of string graphs. It is designed as a modular set of programs used to assemble large genomes from high coverage short read data.

Proper citation: SGA (RRID:SCR_001982) Copy   

•   Source: SciCrunch Registry

http://research-pub.gene.com/gmap/

Software to align single and paired end reads as short as 14 nt and of arbitrarily long length. Can detect short and long distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or database of known splice sites. Permits SNP-tolerant alignment to reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for study of methylation state.

Proper citation: GSNAP (RRID:SCR_005483) Copy   

•   Source: SciCrunch Registry

http://www.emouseatlas.org/emage

A database of in situ gene expression data in the developing mouse embryo and an accompanying suite of tools to search and analyze the data. mRNA in situ hybridization, protein immunohistochemistry and transgenic reporter data is included. The data held is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. The conceptual framework which houses the descriptions of the gene expression patterns in EMAGE is the EMAP Mouse Embryo Anatomy Atlas. This consists of a set of 3D virtual embryos at different stages of development, as well as an accompanying ontology of anatomical terms found at each stage. The raw data images can be conventional 2D photographs (of sections or wholemount specimens) or 3D images of wholemount specimens derived from Optical Projection Tomography (OPT) or confocal microscopy. Users may submit data using a Data submission tool or without.

Proper citation: EMAGE Gene Expression Database (RRID:SCR_005391) Copy   

•   Source: SciCrunch Registry

http://bioinfo.cs.technion.ac.il/atrhunter/

Software that finds and displays approximate tandem repeats in DNA sequences.

Proper citation: ATRHUNTER (RRID:SCR_006480) Copy   

•   Source: SciCrunch Registry

http://last.cbrc.jp/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for aligning sequences, similar to BLAST 2 sequences that colour-codes the alignments by reliability. Another useful feature of LAST is that it can compare huge (vertebrate-genome-sized) datasets. Unfortunately, this only applies to the downloadable version of LAST, not the web service. The web service can just about handle bacterial genomes, but it will take a few minutes and the output will be large. LAST can: * Handle big sequence data, e.g: ** Compare two vertebrate genomes ** Align billions of DNA reads to a genome * Indicate the reliability of each aligned column. * Use sequence quality data properly. * Compare DNA to proteins, with frameshifts. * Compare PSSMs to sequences * Calculate the likelihood of chance similarities between random sequences. LAST cannot (yet): * Do spliced alignment., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LAST (RRID:SCR_006119) Copy   

•   Source: SciCrunch Registry