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https://github.com/davidemms/OrthoFinder

Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format.

Proper citation: OrthoFinder (RRID:SCR_017118) Copy   

•   Source: SciCrunch Registry

https://github.com/mikelove/tximport

Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis.

Proper citation: tximport (RRID:SCR_016752) Copy   

•   Source: SciCrunch Registry

http://cmmt.ubc.ca/facilities-services/mouse-animal-production/

Supplier of mice for research purposes. The service is run by Dr. Elizabeth M. Simpson, Ph.D. and is affiliated with her lab.

Proper citation: CMMT Mouse Animal Production Service (RRID:SCR_016403) Copy   

•   Source: SciCrunch Registry

http://hpc-bioinformatics.cineca.it/stress_mice/

Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data.

Proper citation: Stress Mice Portal (RRID:SCR_017572) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/MetaNeighbor.html

Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting.

Proper citation: MetaNeighbor (RRID:SCR_016727) Copy   

•   Source: SciCrunch Registry

https://omicc.niaid.nih.gov

Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: OMiCC (RRID:SCR_016604) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#bewith

Software tool for discovering relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.

Proper citation: BeWith (RRID:SCR_016573) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/Gsnap2Augustus

Software tool to generate hints for Augustus in ab initio gene prediction using 2 step mapping by Gsnap.

Proper citation: Gsnap2Augustus (RRID:SCR_017555) Copy   

•   Source: SciCrunch Registry

http://www.ifti.org/

A resource for information pertaining to methodologies, tools and technologies of gene expression. The website offers resources for sequence analysis, database services, and other technologies of gene expression and regulation.

Proper citation: IFTI-Mirage (RRID:SCR_000505) Copy   

•   Source: SciCrunch Registry

https://gotrack.msl.ubc.ca/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.jax.org/jax-mice-and-services

Supplier of mice for research purposes.

Proper citation: JAX Mice and Services (RRID:SCR_016408) Copy   

•   Source: SciCrunch Registry

https://www.modelorg.bio/

Global biotechnology company based in Shanghai, China, specializing in custom model organisms, humanized and immunodeficient mice, and gene-editing services for preclinical research. Alternatively, in molecular biology, it can refer to knockout or mutant mice lacking the Smoc1 or Smoc2 genes (secreted modular calcium-binding proteins) used to study embryonic, eye, and limb development.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   

•   Source: SciCrunch Registry

http://www.nrcmm.cn/

Supplier of mice for research purposes.

Proper citation: National Resource Center for Mutant Mice (RRID:SCR_016406) Copy   

•   Source: SciCrunch Registry

https://www.taconic.com/

Supplier of mice for research purposes.

Proper citation: Taconic Biosciences (RRID:SCR_016410) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry