Tools   Select Another Resource Report Type

http://biopp.univ-montp2.fr/wiki/index.php/Main_Page

Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bio++ (RRID:SCR_016055) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

https://ukbec.wordpress.com

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   

•   Source: SciCrunch Registry
  

https://github.com/cerebis/sim3C/tree/0.1

Software for read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC). Sim3C's potential applications include addressing questions directed at the spatial organization of DNA in samples of eukaryotic tissue, single cells, and microbial communities.

Proper citation: Sim3C (RRID:SCR_015772) Copy   

•   Source: SciCrunch Registry
  

https://github.com/thegenemyers/DAZZ_DB

Software library and database to manage nucleotide sequencing read data. It stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files and avoid duplicating data.

Proper citation: Dazzler (RRID:SCR_016069) Copy   

•   Source: SciCrunch Registry
  

https://www.norpix.com/products/streampix/streampix.php

Software for digital video camera recording that allows users to control and acquire dadta from multiple cameras simultaneously in a singleuser interface. StreamPix provides a complete management console for cameras, simplifying the setup, control and acquisition from any number and type of camera.

Proper citation: StreamPix (RRID:SCR_015773) Copy   

•   Source: SciCrunch Registry
  

http://www.syngene.com/genesys-2/

Imaging software that works with G:BOX Chemi and PXi imaging systems to automatically or manually capture images. GeneSys also includes a database containing information about applications such as fluorescence, chemiluminescence and chemifluorescence.

Proper citation: GeneSys (RRID:SCR_015770) Copy   

•   Source: SciCrunch Registry
  

http://scit.us/projects/dawg

Software application to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation. The application accepts phylogenies in Newick format and can return the sequence of any node, allowing for the exact evolutionary history to be recorded at the discretion of users.

Proper citation: Dawg (RRID:SCR_016068) Copy   

•   Source: SciCrunch Registry
  

https://genome.tugraz.at/genesisclient/genesisclient_description.shtml

Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments.

Proper citation: Genesis (RRID:SCR_015775) Copy   

•   Source: SciCrunch Registry
  

http://boinc.berkeley.edu

Software to orchestrate the distribution of computational work units (data and applications) to volunteers and have results collected back. It supports diverse applications, including those with large storage or communication requirements, and addresses unsolved issues in biology, medicine, physics, astronomy and computer science.

Proper citation: BOINC - Berkeley Open Infrastructure for Network Computing (RRID:SCR_015896) Copy   

•   Source: SciCrunch Registry
  

http://www.xavierdidelot.xtreemhost.com/clonalframe.htm

Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.

Proper citation: Clonalframe (RRID:SCR_016060) Copy   

•   Source: SciCrunch Registry
  

https://dazzlerblog.wordpress.com

Software alignment tool to find all significant local alignments between long and noisy, up to 15% on average reads encoded in a Dazzler database. Used for DNA sequence assembly, specifically for next generation long-read sequencers such as the Pacbio RS II and Sequel sequencers.

Proper citation: Daligner (RRID:SCR_016066) Copy   

•   Source: SciCrunch Registry
  

https://www.icpsr.umich.edu/icpsrweb/content/addep/index.html

Provides access to data including wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of Americans with Disabilities Act and other disability policies.

Proper citation: Archive of Data on Disability to Enable Policy (ADDEP) (RRID:SCR_016315) Copy   

•   Source: SciCrunch Registry
  

http://aphasia.talkbank.org/

Shared database of multimedia interactions for the study of communication in aphasia.Access to the data in AphasiaBank is password protected and restricted to members of the AphasiaBank consortium group.

Proper citation: AphasiaBank (RRID:SCR_016317) Copy   

•   Source: SciCrunch Registry
  

https://hirnetwork.org/consortium/ctar

Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is investigating methods to increase or maintain functional beta cell mass in T1D through targeted manipulation of islet plasticity or engineered protection of beta cells from immune-mediated destruction.

Proper citation: HIRN Consortium on Targeting and Regeneration (RRID:SCR_016201) Copy   

•   Source: SciCrunch Registry
  

http://www.omicsbean.cn

Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users.

Proper citation: OmicsBean (RRID:SCR_016322) 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