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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Laboratory portal of the University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory.
Proper citation: USP Molecular Genetics and Bioinformatics Laboratory (RRID:SCR_000605) Copy
https://github.com/WangHYLab/fcirc
Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs.
Proper citation: Fcirc (RRID:SCR_018090) Copy
https://health.uconn.edu/worm-lab/track-a-worm/
Open source system for quantitative assessment of C. Elegans locomotory and bending behavior. Used for quantitative behavioral analyses to understand circuit and gene bases of behavior. Constantly records and analyzes position and body shape of freely moving worm at high magnification.
Proper citation: Track-A-Worm (RRID:SCR_018299) Copy
Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis.
Proper citation: Database of Immune Cell Epigenomes (RRID:SCR_018259) Copy
https://metacpan.org/pod/Bio::CUA
Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems.
Proper citation: Codon Usage Analyzer (RRID:SCR_018500) Copy
https://bioconductor.org/packages/minet/
Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data.
Proper citation: minet (RRID:SCR_018661) Copy
Web service for querying or retrieving gene annotation data.
Proper citation: MyGene.info (RRID:SCR_018660) Copy
Web service that conducts comprehensive literature mining to identify roles of genes in addiction. Searches PubMed to find abstracts containing genes of interest and list of curated addiction related keywords.
Proper citation: RatsPub (RRID:SCR_018905) Copy
http://tools.dice-database.org/GOnet/)
Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.
Proper citation: GOnet (RRID:SCR_018977) Copy
Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are.
Proper citation: miRpathDB (RRID:SCR_017356) Copy
Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms.
Proper citation: SynGO (RRID:SCR_017330) Copy
http://promoter.bx.psu.edu/hi-c/
Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: 3D Genome (RRID:SCR_017525) Copy
https://github.com/tanghaibao/mcscan
Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format.
Proper citation: MCScan (RRID:SCR_017650) Copy
https://github.com/gdancik/shinyGEO
Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets.
Proper citation: shinyGEO (RRID:SCR_017605) Copy
https://scdevdb.deepomics.org/
Database for insights into single cell gene expression profiles during human developmental processes. Interactive database provides DE gene lists in each developmental pathway, t-SNE map, and GO and KEGG enrichment analysis based on these differential genes.
Proper citation: Single Cell Developmental Database (RRID:SCR_017546) Copy
https://github.com/LaBiOS/Transcriptive
Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results.
Proper citation: Transcriptive (RRID:SCR_017545) Copy
https://ihg.helmholtz-muenchen.de/cgi-bin/hw/hwa1.pl
Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases.
Proper citation: Tests for deviation from Hardy-Weinberg equilibrium (RRID:SCR_016496) Copy
http://homer.ucsd.edu/homer/microarray/index.html
Software tool to analyze the promoters of genes and look for motifs that are enriched in the target gene promoters relative to other promoters. Used for gene based analysis to provide a list of genes that should contain the same elements, such as genes that are co-regulated. It includes gene ontology analysis and can be used to look for RNA motifs in mRNAs.
Proper citation: findMotif.pl (RRID:SCR_016417) Copy
http://amp.pharm.mssm.edu/DGB/
Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures.
Proper citation: Drug Gene Budger (RRID:SCR_016489) Copy
https://www.thermofisher.com/order/catalog/product/00-0210
Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis.
Proper citation: Thermo Fisher: GeneChip� Scanner 3000 7G (RRID:SCR_016522) Copy
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