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http://nematode.lab.nig.ac.jp/
Expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from their expression pattern project and to make the data available to the scientific community. Information available in the current version is as follows: * Map: Visual expression of the relationships among the cosmids, predicted genes and the cDNA clones. * Image: In situ hybridization images that are arranged by their developmental stages. * Sequence: Tag sequences of the cDNA clones are available. * Homology: Results of BLASTX search are available. Users of the data presented on our web pages should not publish the information without our permission and appropriate acknowledgment. Methods are available for: * In situ hybridization on whole mount embryos of C.elegans * Protocols for large scale in situ hybridization on C.elegans larvae
Proper citation: NEXTDB (RRID:SCR_004480) Copy
http://bioinf.wehi.edu.au/limma/
Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.
Proper citation: LIMMA (RRID:SCR_010943) Copy
http://pathways.mcdb.ucla.edu/algal/
Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest.
Proper citation: Algal Functional Annotation Tool (RRID:SCR_012034) Copy
http://bioconductor.org/packages/edgeR/
Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
Proper citation: edgeR (RRID:SCR_012802) Copy
Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
Proper citation: KEGG (RRID:SCR_012773) Copy
https://github.com/harry-thorpe/piggy
Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary).
Proper citation: Piggy (RRID:SCR_015941) Copy
http://www.genetherapyreview.com/gene-therapy-research
The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies.
Proper citation: National Gene Vector Laboratories (RRID:SCR_015944) Copy
Consortium studying the regulation and alternative splicing of gene expression in multiple tissues from human brains. The UKBEC dataset comprises of brains from individuals free of neurodegenerative disorders.
Proper citation: UK Brain Expression Consortium (RRID:SCR_015889) Copy
http://amp.pharm.mssm.edu/l1000fwd/
Web application that provides interactive visualization of drug and small-molecule induced gene expression signatures. L1000FWD enables coloring of signatures by different attributes such as cell type, time point, concentration, as well as drug attributes such as MOA and clinical phase.
Proper citation: L1000 Fireworks Display (RRID:SCR_016175) Copy
http://baderlab.org/Software/EnrichmentMap
Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together.
Proper citation: EnrichmentMap (RRID:SCR_016052) Copy
http://amp.pharm.mssm.edu/LJP/
Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations.
Proper citation: LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) Copy
Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.
Proper citation: GOTrack (RRID:SCR_016399) Copy
https://github.com/Sung-Huan/ANNOgesic
Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.
Proper citation: ANNOgesic (RRID:SCR_016326) Copy
Supplier of mice for research purposes. Provides technical services, model organisms, gene editing and decoding.
Proper citation: Shanghai Model Organisms Center (RRID:SCR_016407) Copy
Supplier of mice for research purposes.
Proper citation: National Resource Center for Mutant Mice (RRID:SCR_016406) 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://github.com/alesssia/YAMP
Software for processing and analysis of sequencing data. It has a strong focus on quality control, timely processing, functional annotation, and portability.
Proper citation: YAMP (RRID:SCR_016236) Copy
http://www.fishbrowser.org/software/LR_Gapcloser/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th, 2023. Software that uses long reads to close gaps in the assemblies.
Proper citation: LR Gapcloser (RRID:SCR_016194) 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://www.jax.org/jax-mice-and-services
Supplier of mice for research purposes.
Proper citation: JAX Mice and Services (RRID:SCR_016408) Copy
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