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http://knowtator.sourceforge.net/
A general-purpose text annotation tool that is integrated with the Prot����g���� knowledge representation system.
Proper citation: Knowtator (RRID:SCR_012099) Copy
http://sourceforge.net/projects/pb-jelly/
Software that automates the finishing process using long sequence reads in a reference-guided assembly process.
Proper citation: PBJelly (RRID:SCR_012091) Copy
https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/AHA
Contigs from a draft assembly generated by a different assembler can be joined using PacBio long reads.
Proper citation: AHA (RRID:SCR_012090) Copy
https://code.google.com/p/netcoffee/
A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.
Proper citation: NetCoffee (RRID:SCR_012095) Copy
https://code.google.com/p/qsimscan/
A flexible open source protein similarity search software tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss.
Proper citation: PSimScan (RRID:SCR_012094) Copy
http://www.few.vu.nl/~mavdwiel/ShrinkBayes.html
Software for detecting differential features across the entire spectrum, including the lower counts.
Proper citation: ShrinkSeq (RRID:SCR_012022) Copy
http://www.stat.purdue.edu/~doerge/software/TSPM.R
Software using a statistical approach, based on a two-stage Poisson model, for modeling RNA sequencing data and testing for biologically important changes in gene expression.
Proper citation: TSPM.R (RRID:SCR_012021) Copy
A genome browser specialized in next-generation sequencing data.
Proper citation: GenomeJack (RRID:SCR_012026) Copy
http://www.nature.com/nmeth/journal/v5/n3/extref/nmeth.1184-S2.pdf
Software for decoding error-correcting barcodes.
Proper citation: Standalone hamming (RRID:SCR_012025) Copy
http://www.compudrug.com/toxalert
Software tool for high-throughput toxicity prediction; it assists in the early and quick identification of toxic drug candidates. ToxAlert provides probability percentages for different toxicity endpoints such as oncogenicity, mutagenicity, teratogenicity, neurotoxicity or cell toxicity.
Proper citation: ToxAlert (RRID:SCR_014907) Copy
http://bioinformatics.psb.ugent.be/orcae/
Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community.
Proper citation: Online Resource for Community Annotation of Eukaryotes (RRID:SCR_014989) Copy
https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFADBMBCX
Mass spectrometer that combines quadrupole, ion trap, and Orbitrap mass analysis.
Proper citation: LTQ-Orbitrap Fusion Tribrid Mass Spectrometer (RRID:SCR_014992) Copy
https://www.nikoninstruments.com/en_EU/Products/Upright-Microscopes/Research/Eclipse-FN1
Fixed-stage microscope for electrophysiological research. Features include open design, noise reduction, 16x objective lens, and water dipping objective with depth induced aberration correction.
Proper citation: Nikon: Eclipse FN1 Microscope (RRID:SCR_014995) Copy
Private organization that offers resources and serves as a community for those recovering from addiction and to help patients find the highest quality care for a successful recovery.
Proper citation: AddictionResources (RRID:SCR_015048) Copy
https://www.agilent.com/cs/library/datasheets/Public/5991-2541EN.pdf
Hardware system which automates RNA, DNA, and protein sample QC, including sample loading, separation, and imaging.
Proper citation: Agilent: 2200 TapeStation Instrument (RRID:SCR_014994) Copy
Regional commission of the United Nations with the purpose of contributing to the economic development of Latin America, coordinating actions directed towards this end, reinforcing economic ties among countries and with other nations, and promoting social development.
Proper citation: Economic Commission for Latin America and the Caribbean (RRID:SCR_014998) Copy
http://www.multicase.com/meta-pc
Software program to predict metabolic and degradation products of chemicals. METAPC has dictionaries on mammalian metabolism, aerobic microbial degredation, anerobic microbial degredation, and photo degredation.
Proper citation: METAPC (RRID:SCR_014916) Copy
https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
Conversion software developed by Illumina that both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
Proper citation: bcl2fastq (RRID:SCR_015058) Copy
Foundation for improving the quality of life for people affected by OI through treatment and cure research, education, awareness, and mutual support. OIF lists personal resources for individuals affected by osteogenesis imperfecta as well as professional and clinical resources for researchers.
Proper citation: Osteogenesis Imperfecta Foundation (RRID:SCR_015034) Copy
https://www.cdc.gov/labstandards/index.html
Standardization program which helps assure the quality of laboratory test data and results so patients, healthcare providers, researchers, and public health officials can be confident that laboratory test results they receive are accurate. CDC services include reference materials, proficiency testing, training, guideline creation, and consultations. Quality assurance and standardization programs can be can be customized by and for users and laboratories.
Proper citation: CDC Laboratory Quality Assurance and Standardization Programs (RRID:SCR_015000) Copy
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