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https://amp.pharm.mssm.edu/geneshot/

Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations.

Proper citation: Geneshot (RRID:SCR_017582) Copy   

•   Source: SciCrunch Registry

http://geneontology.org/docs/go-consortium/

Consortium integrates resources from variety of research groups, from model organisms to protein databases to biological research communities actively involved in development and implementation of Gene Ontology. Mission to develop up to date, comprehensive, computational model of biological systems, from molecular level to larger pathways, cellular and organism level systems.

Proper citation: GO Gene Ontology Consortium and Knowledgebase (RRID:SCR_017505) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/mgihome/nomen/index.shtml

Authoritative source of official names for mouse genes, alleles, and strains. Nomenclature follows rules and guidelines established by International Committee on Standardized Genetic Nomenclature for Mice.

Proper citation: Nomenclature (RRID:SCR_017511) Copy   

•   Source: SciCrunch Registry

https://www.jax.org/research-and-faculty/resources/knockout-mouse-project

Information from JAX about their contributions to KOMP project coordinated by International Mouse Phenotyping Consortium. National Institutes of Health has funded three KOMP2 centers in United States, including one at Jackson Laboratory, to work together on task of producing and phenotyping mice to establish resource of knockout mice and related database of gene function.

Proper citation: Knockout Mouse Project Repository at JAX (RRID:SCR_017512) Copy   

•   Source: SciCrunch Registry

http://sydney.edu.au/medicine/bosch/facilities/molecular-biology/nucleic-acid/corbett-rotor-gene.php

Rotor-Gene real-time analysis software system for ROTOR GENE 6000 REAL-TIME PCR machine. Software has been refined to provide an intuitive, Wizard driven interface, enabling flexibility and automation. Build-in extensive analysis, graphing and statistical functions. Unlimited use software license for Windows XP, Pentium IV (2GHz) or higher PC.

Proper citation: Rotor-Gene 6000 series software (RRID:SCR_017552) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/scater.html

Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data.

Proper citation: scater (RRID:SCR_015954) Copy   

•   Source: SciCrunch Registry

https://github.com/cyaguesa/SL-quant/

Source code for a bash pipeline that quantifies splice-leader (SL) trans-splicing events by genes in the nematode C. elegans. It is designed to work downstream of read mapping and takes the reads left unmapped as primary input.

Proper citation: SL-quant (RRID:SCR_016205) Copy   

•   Source: SciCrunch Registry

http://www.functionalnet.org/humannet/about.html

Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes.

Proper citation: HumanNet (RRID:SCR_016146) Copy   

•   Source: SciCrunch Registry

http://homes.gersteinlab.org/Khurana-PLoSCompBio-2013/

Software for an integrated network combining multiple biological network database sources into a single human protein interactome. The software package contains gene interaction pairs corresponding to the unified global network.

Proper citation: MultiNet (RRID:SCR_016149) Copy   

•   Source: SciCrunch Registry

https://github.com/Oshlack/Clinker/wiki

Software for a bioinformatics pipeline that generates a superTranscriptome from popular fusion finder outputs (JAFFA, tophatFusion, SOAP, deFUSE, Pizzly, etc). They can be then be either viewed in genome viewers such as IGV or through the included plotting feature developed with GViz.

Proper citation: Clinker (RRID:SCR_016140) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/L1000CDS2

LINCS L1000 characteristic direction signatures search engine. Software tool to find consensus signatures that match user’s input gene lists or input signatures. Underlying dataset is LINCS L1000 small molecule expression profiles generated at Broad Institute by Connectivity Map team. Differentially expressed genes of these profiles were calculated using multivariate method called Characteristic Direction.

Proper citation: L1000 Characteristic Direction Signature Search Engine (RRID:SCR_016177) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/Harmonizome/

Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources.

Proper citation: Harmonizome (RRID:SCR_016176) Copy   

•   Source: SciCrunch Registry

https://isi.edu/integration/people/chunnan/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 14, 2018. An XML-RPC client of a web-service server which provides the service to recognize named entities in the biomedical articles. It is Gene Mention Tagger (GMT) for Biological Text Mining.

Proper citation: AIIA-GMT (RRID:SCR_016397) Copy   

•   Source: SciCrunch Registry

https://gemma.msl.ubc.ca/phenotypes.html

Database that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. Part of Gemma, a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data.

Proper citation: Phenocarta (RRID:SCR_016273) Copy   

•   Source: SciCrunch Registry

http://aspiredb.msl.ubc.ca/

Web based software for analyzing genomic variants CNVs, SNVs, and Indels and phenotypes. It aims to represent the relationships between discovered variants and phenotypes.

Proper citation: AspireDB (RRID:SCR_016272) Copy   

•   Source: SciCrunch Registry

http://www.nlac.org.tw/RMRC/index_e.aspx

Supplier of mice for research purposes.

Proper citation: National Applied Research Laboratories (RRID:SCR_016405) Copy   

•   Source: SciCrunch Registry

https://www.jax.org/research-and-faculty/resources/oak-ridge-strains#

Supplier of mice for research purposes.

Proper citation: Oak Ridge Collection at JAX (RRID:SCR_016409) Copy   

•   Source: SciCrunch Registry

http://www.myv.ne.jp/obs/

Supplier of mice for research purposes.

Proper citation: Oriental BioService Inc. (RRID:SCR_016404) Copy   

•   Source: SciCrunch Registry

http://cole-trapnell-lab.github.io/monocle-release/docs/

Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations.

Proper citation: Monocle2 (RRID:SCR_016339) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/geo/info/geo2r.html

Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance.

Proper citation: GEO2R (RRID:SCR_016569) Copy   

•   Source: SciCrunch Registry