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https://github.com/lkmklsmn/DrivAER

Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data.

Proper citation: DrivAER (RRID:SCR_019076) 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
  

http://www.imgt.org/HighV-QUEST/home.action

Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing.

Proper citation: IMGT HighV-QUEST (RRID:SCR_018196) Copy   

•   Source: SciCrunch Registry
  

https://gat.readthedocs.io/en/latest/

Software tool as simulation framework for testing association of genomic intervals. Used for estimating significance of overlap between multiple sets of genomic intervals. Estimates statistical significance based on simulation and controls for multiple tests using false discovery rate.

Proper citation: Genomic Association Tester (RRID:SCR_020949) Copy   

•   Source: SciCrunch Registry
  

https://pm4ngs.readthedocs.io/

Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution.

Proper citation: PM4NGS (RRID:SCR_019164) 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://www.creative-peptides.com/services/formulation-development.html

Service to determine optimal dosage form, composition and manufacturing route for pharmaceutical products.

Proper citation: Creative Peptides: Formulation Development Service Resource (RRID:SCR_022223) Copy   

•   Source: SciCrunch Registry
  

https://www.creative-peptides.com/services/peptide-lead-optimization.html

Provides optimized one stop solution for peptide lead drugs. Used to improve upon lead molecule that demonstrates activity at target of interest by optimizing its potency or selectivity at target and its absorption, distribution, metabolism and elimination properties.

Proper citation: Creative Peptides: Peptide Lead Optimization Service Resource (RRID:SCR_022222) Copy   

•   Source: SciCrunch Registry
  

https://www.creative-peptides.com/services/peptide-drug-bioconjugations.html

Custom peptide synthesis, modification, and conjugation services involve chemical modification of peptide at highly specific sites. This allows for attachment of drugs or bioactive molecules though variety of coupling techniques.

Proper citation: Creative Peptides Peptide Drug Bioconjugations Service Resource (RRID:SCR_022221) 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
  

http://neomorph.salk.edu/omb/

Viewer for DNA Methylation Atlas of Mouse Brain at Single Cell Resolution. Browser to interactively explore single cell methylome dataset including exploration of methylation diversity of one gene at single-cell or cell-type level, exploration of cell type composition of adult mouse brain dissection regions and anatomical structures, explorartion of spatial distribution and methylation signature genes of one cell type.

Proper citation: Brain Cell Methylation Viewer (RRID:SCR_020954) Copy   

•   Source: SciCrunch Registry
  

https://www.creative-peptides.com/services/total-peptide-library-construction-technology.html

Service uses bioinformatics methods to compress peptide information, which can integrate information of multiple peptide into one peptide. Provides collection of small peptide of specific length and different sequences, which includes permutation and combination of various amino acid sequences in short peptide of this length.Total peptide library for new drug research and development.

Proper citation: Creative Peptides Total Peptide Library Construction Service Resource (RRID:SCR_022219) Copy   

•   Source: SciCrunch Registry
  

https://mass-spec.stanford.edu/instruments

System includes SQD2 as single quadrupole MS with Waters H-Class Acquity UPLC, operated as open access platform for trained users. SQ Detector2 is single quadrupole mass detector for chromatography compatible with range of chromatography platforms and ionization sources.

Proper citation: Waters: SQD2 LC/MS system (RRID:SCR_022217) Copy   

•   Source: SciCrunch Registry
  

http://old.protein.bio.unipd.it/cspritz/

Web tool for prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs.

Proper citation: CSpritz (RRID:SCR_021884) Copy   

•   Source: SciCrunch Registry
  

https://signor.uniroma2.it/

Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles.

Proper citation: SIGNOR (RRID:SCR_018485) Copy   

•   Source: SciCrunch Registry
  

https://shimadzu.com.au/labsolutions

Software package for data analysis by Shimadzu Oceania.

Proper citation: LabSolutions (RRID:SCR_018241) Copy   

•   Source: SciCrunch Registry
  

http://g2d2.ogic.ca

The Institute for Advanced Biosciences, Keio University, is an academic research institute pioneering the new life science field of Systems Biology, using both experimental and computational biology. There are several groups working in collaboration, focusing mainly on genome biology and engineering, genome design and synthetic biology, metabolic engineering, proteomics, metabolomics, RNA biology, bioinformatics and computational biology. Using cutting-edge technologies, intracellular components can be analyzed comprehensively to construct computer simulation models that can find numerous applications in fields such as biomedical, environmental, and agricultural science. Experimental and computational facilities are located in Tsuruoka, Yamagata prefecture, in northern Japan while the SFC campus, in the Tokyo area, hosts the bioinformatics laboratory and most undergraduate curricular activities. IAB has successfully attracted very significant funding for multiple research projects from major funding organizations including the New Energy and Industrial Technology Development Organization (NEDO) (2002-2006), for bioprocesses and cell modeling, the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and its COE network, for biosimulation and systems biology (2003-2008), the Japan Science and Technology Agency (CREST, 2004-2009) for simulation and systems biology, the Ministry of Health, for cancer biology (2005), as well as from Yamagata prefecture and Tsuruoka city, 2001-2006 and 2006-2011). Over the past few years, IAB scientists have accumulated several awards including the 1st prize during the 5th Japan Biotechnology Business Competition (2005), the Minister of State for Science and Technology Policy award in recognition for industry-academia-government collaboration performance (2004), the IBM Shared University Research Award (2003), and the Nihon Kogyo Shimbunsha Award (2003) during the 17th Leading-edge Technology for Originality and Creativity. Sponsor. This study was supported by a grant from the Global COE Program entitled, Human Metabolomic Systems Biology and by a Grant-in-Aid for Scientific Research on Priority Areas Systems Genomes and on Lifesurveyor from the Ministry of Education, Culture, Sports, Science and Technology of Japan as well as research funds from the Yamagata prefectural government and the City of Tsuruoka.

Proper citation: Institute for Advanced Biosciences (RRID:SCR_008526) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/fadtts/

Pipeline developed for delineating the association between multiple diffusion properties along major white matter fiber bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these white matter tract properties in various diffusion tensor imaging studies. FADTTS can be used to facilitate understanding of normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. The advantages of FADTTS compared with the other existing approaches are that they are capable of modelling the structured inter-subject variability, testing the joint effects, and constructing their simultaneous confidence bands.

Proper citation: Functional Analysis of Diffusion Tensor (RRID:SCR_008888) Copy   

•   Source: SciCrunch Registry
  

http://galton.uchicago.edu/~junzhang/LAPSTRUCT.html

Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software)

Proper citation: LAPSTRUCT (RRID:SCR_007550) Copy   

•   Source: SciCrunch Registry
  

http://www.floridaaquaculture.com

This web site is your introduction to the world of Florida Aquaculture. It represents a compilation of information about a division in the Florida Department of Agriculture and Consumer Services-the Division of Aquaculture. The Division plays a key role in the regulation of aquaculture facilities and shellfish processing plants, is responsible for opening/closing of shellfish harvesting waters to protect human health, ensures the continued productivity of oyster reefs through a restoration program and issues leases of submerged state lands for aquaculture. The creation of this division is unprecedented for a state agriculture department. Florida''s Division of Aquaculture is one-of-a-kind and serves a unique industry like no other in the United States. Please browse this site and learn more about Florida Aquaculture. I welcome your comments on the topics contained in this web site.

Proper citation: Division of Aquaculture (RRID:SCR_008484) Copy   

•   Source: SciCrunch Registry