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Supplier of mice for research purposes.
Proper citation: National Resource Center for Mutant Mice (RRID:SCR_016406) Copy
Supplier of mice for research purposes.
Proper citation: Taconic Biosciences (RRID:SCR_016410) Copy
https://www.genomics.agilent.com/article.jsp?pageId=2100
Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MxPro QPCR (RRID:SCR_016375) 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://github.com/sblanck/smagexp
Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more.
Proper citation: SMAGEXP (RRID:SCR_016360) Copy
https://github.com/WGS-TB/MentaLiST
Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.
Proper citation: MentaLiST (RRID:SCR_016469) Copy
https://github.com/umerijaz/nanopore
Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing.
Proper citation: NanoAmpli-Seq (RRID:SCR_016710) Copy
https://github.com/iychoi/libra
Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples.
Proper citation: Libra (RRID:SCR_016608) Copy
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000363.v16.p10
Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation.
Proper citation: SABRe CVD Initiative (RRID:SCR_016572) Copy
https://www.stemformatics.org/#
Gene expression data portal developed for stem cell community, containing public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Portal to visualize and download curated stem cell data. Provides easy to use and intuitive tools for biologists to visually explore data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others.
Proper citation: Stemformatics (RRID:SCR_017002) Copy
http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.
Proper citation: clusterProfiler (RRID:SCR_016884) 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
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
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
https://github.com/lucapinello/Haystack
Software suite of computational tools implemented in Python to study epigenetic variability, cross cell type plasticity of chromatin states and transcription factors motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation. Epigenetic variability and transcription factor motifs analysis pipeline.
Proper citation: Haystack (RRID:SCR_017087) Copy
https://github.com/im3sanger/dndscv
Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets.
Proper citation: dndSCV (RRID:SCR_017093) Copy
http://bioconductor.org/packages/gage/
Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies.
Proper citation: GAGE (RRID:SCR_017067) Copy
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