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https://cgb.indiana.edu

CGB offers range of genomic services, including high-throughput DNA/RNA extraction, library preparation, next-generation sequencing, and bioinformatic analysis.

Proper citation: Indiana University Center for Genomics and Bioinformatics Core Facility (RRID:SCR_017165) Copy   

•   Source: SciCrunch Registry
  

https://www.ncbi.nlm.nih.gov/labs/virus/vssi

Community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories. Integrative, value added resource designed to support retrieval, display and analysis of curated collection of virus sequences and large sequence datasets. Used to increase usability of data archived in GenBank and other NCBI repositories.

Proper citation: NCBI Virus (RRID:SCR_018253) Copy   

•   Source: SciCrunch Registry
  

https://tmcalculator.neb.com/#!/main

Calculator to estimate appropriate annealing temperature when using NEB PCR products.Tm calculator provided by New England Biolabs.

Proper citation: NEB Tm calculator (RRID:SCR_017969) Copy   

•   Source: SciCrunch Registry
  

https://www.ncbi.nlm.nih.gov/sutils/pasc/viridty.cgi

Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database.

Proper citation: PASC (RRID:SCR_016642) Copy   

•   Source: SciCrunch Registry
  

https://edspace.american.edu/openbehavior/project/3doc/

Project related to animals learned perform action in order to achieve reward. Fully 3D printable chamber able to perform operant conditioning using off-the-shelf, low-cost optical and electronic components, that can be reproduced rigorously in any laboratory equipped with 3D printer.

Proper citation: 3DOC (RRID:SCR_021547) 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://ccg.vital-it.ch/snp2tfbs

Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs.

Proper citation: SNP2TFBS (RRID:SCR_016885) Copy   

•   Source: SciCrunch Registry
  

https://www.hopkinsmedicine.org/institute-basic-biomedical-sciences/services/single-cell-sequencing-transcriptomics-core

Core provides assistance with Single Cell RNA and DNA Sequencing, Spatial Transcriptomics, Next-Generation Sequencing libraries.

Proper citation: Johns Hopkins Medicine Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core Facility (RRID:SCR_017172) Copy   

•   Source: SciCrunch Registry
  

http://home.cc.umanitoba.ca/~frist/Bit/

BIT Core at University of Manitoba, Manitoba, Canada, provides bioinformatics services, resources and collaborations. Support for Genome assembly and annotation, Microarray and Transcriptomics, Systems Biology and Pathway analysis, Databases, Data pipelines, Bioinformatics software, Custom software and programming, Project Wikis, Lab group computer management.

Proper citation: University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility (RRID:SCR_017177) Copy   

•   Source: SciCrunch Registry
  

https://github.com/broadinstitute/Drop-seq

Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript.

Proper citation: Drop-seq tools (RRID:SCR_018142) 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://github.com/CEGRcode/stencil

Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise.

Proper citation: STENCIL (RRID:SCR_021878) Copy   

•   Source: SciCrunch Registry
  

https://opticalmapping.info

Platform to provide tutorials and resources in experimental design and data analysis to researchers interested in using optical mapping data.

Proper citation: OpticalMapping.info (RRID:SCR_017146) Copy   

•   Source: SciCrunch Registry
  

https://glimmpse.samplesizeshop.org/#/

Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering.

Proper citation: GLIMMPSE (RRID:SCR_016297) Copy   

•   Source: SciCrunch Registry
  

https://github.com/gtonkinhill/panaroo

Software pipeline for pangenome investigation. Shares information between genomes to correct errors. Can call large structural variants.Fast and scalable to over 10k bacterial genomes.

Proper citation: Panaroo (RRID:SCR_021090) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Benson-Genomics-Lab/TRF

Software tool to locate and display tandem repeats in DNA sequences. Used to analyze DNA sequences.

Proper citation: Tandem Repeats Finder (RRID:SCR_022065) Copy   

•   Source: SciCrunch Registry
  

https://github.com/sreeramkannan/Shannon

Software tool for de novo transcriptome assembly from RNA-Seq data.

Proper citation: Shannon (RRID:SCR_017037) Copy   

•   Source: SciCrunch Registry
  

https://github.com/neurostuff/NiMARE

Software Python package for coordinate and image based meta analysis of neuroimaging data.

Proper citation: NiMARE (RRID:SCR_017398) Copy   

•   Source: SciCrunch Registry
  

https://www.iconplc.com/innovation/nonmem/

Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions.

Proper citation: NONMEM (RRID:SCR_016986) Copy   

•   Source: SciCrunch Registry