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https://ihg.gsf.de/ihg/mitoprot.html

Web server for prediction of mitochondrial targeting sequences.

Proper citation: Mitoprot (RRID:SCR_019023) Copy   

•   Source: SciCrunch Registry

http://genometools.org/

Software tool for de novo detection of full length LTR retrotransposons in large sequence sets. Delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs.

Proper citation: LTRharvest (RRID:SCR_018970) Copy   

•   Source: SciCrunch Registry

https://zlab.bio/guide-design-resources

Laboratory portal about research including new approaches for precision gene editing, delivery of molecular and genetic cargo, discovery of novel programmable systems, and engineering of immune system to develop next generation of therapeutics. Provides collection of tools for guide design.CRISPR.MIT.EDU of Guide Design Tools is no longer available, documented on August 28,2020.

Proper citation: Guide Design Resources (RRID:SCR_018982) Copy   

•   Source: SciCrunch Registry

https://www.bio-rad.com/en-in/product/chemidoc-mp-imaging-system?ID=NINJ8ZE8Z

Instrument for imaging and analyzing gels and western blots by Bio Rad. Designed to address multiplex fluorescent western blotting, chemiluminescence detection, general gel documentation applications, and stain-free technology imaging needs.

Proper citation: Bio-Rad: ChemiDoc MP Imaging System (RRID:SCR_019037) Copy   

•   Source: SciCrunch Registry

https://idseq.net/

Open source cloud based pipeline and analysis service for metagenomic pathogen detection and monitoring. Hypothesis free global software platform that helps scientists identify pathogens in metagenomic sequencing data. IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes assembly based alignment pipeline which results in assignment of reads and contigs to taxonomic categories.

Proper citation: IDseq (RRID:SCR_019038) Copy   

•   Source: SciCrunch Registry

https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation

Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer.

Proper citation: CLIP Tool Kit (RRID:SCR_019034) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com/en/product/software-informatics/mass-spectrometry-software/data-analysis/qualitative-analysis

Mass spectrometry screening software for confirmation of target or suspect compounds, and for identification of unknown analytes. Advanced data mining and processing options let find all detectable compounds and confirm targets or identify unknowns. Results can be displayed using data reporting with either preconfigured reports that simplify basic analyses, or completely customized PDF reports.

Proper citation: Agilent MassHunter Qualitative Analysis (RRID:SCR_019081) Copy   

•   Source: SciCrunch Registry

https://www.norlab.com/library/brochure/11566

Multi channel peristaltic pump for applications with different viscous or abrasive fluids. Allows for channel cartridges, from one to sixteen, to be changed while pump is running.

Proper citation: Gilson: Minipuls Evolution peristaltic pump (RRID:SCR_018955) Copy   

•   Source: SciCrunch Registry

https://www.harvardapparatus.com/tabletop-anesthesia-systems.html#collapseTwo

Tabletop anesthesia system suitable for mice, rats and other small animals under 10 lb. Passive scavenging systems. Funnel fill isoflurane vaporizers.

Proper citation: Harvard Apparatus: Single Animal Tabletop Isoflurane Anesthesia System with Small Induction Box (RRID:SCR_018956) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/vmas_2020/

Software tool to generate whole connected 3D brain ventricular shape model and encode ventricular surface deformation information that is inaccessible by ventricle volume measure. Contains automated segmentation approach and surface based multivariate morphometry statistics.

Proper citation: Ventricular Morphometry Analysis System (RRID:SCR_019007) Copy   

•   Source: SciCrunch Registry

https://opencor.ws/

Open source cross platform modeling environment for reproducible science. Used to organise, edit, simulate and analyse models described in CellML format, using SED-ML and COMBINE archives.

Proper citation: OpenCOR (RRID:SCR_019001) Copy   

•   Source: SciCrunch Registry

http://enterobase.warwick.ac.uk/

Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella.

Proper citation: EnteroBase (RRID:SCR_019019) Copy   

•   Source: SciCrunch Registry

http://dgenies.toulouse.inra.fr/

Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.

Proper citation: D-GENIES (RRID:SCR_018967) Copy   

•   Source: SciCrunch Registry

http://amphibian.hiroshima-u.ac.jp/english/ARC_HP_English_ver./english_page.html

Stock center that provides amphibian organisms, frogs and newts, primarily to Japanese investigators. The center runs the National BioResource Project (NBRP) Clawed frogs / Newts, which is financially supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, to distribute these resources. Contributes to maintenance of biologically important strains of frogs and study biological characteristics of amphibian focusing genetics, developmental regulation, speciation, phylogeny, phenotype expression, and environment-induced mutagenesis.

Proper citation: Hiroshima University Amphibian Research Center (RRID:SCR_019015) Copy   

•   Source: SciCrunch Registry

https://www.crd.york.ac.uk/PROSPERO

International database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is health related outcome. Key features from review protocol are recorded and maintained as permanent record. Aims to provide comprehensive listing of systematic reviews registered at inception to help avoid duplication and reduce opportunity for reporting bias by enabling comparison of completed review with what was planned in protocol.

Proper citation: PROSPERO (RRID:SCR_019061) Copy   

•   Source: SciCrunch Registry

http://www.softberry.com/berry.phtml?topic=fgenesh_plus_plus&group=help&subgroup=pipelines

Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software.

Proper citation: Fgenesh plus plus (RRID:SCR_018928) Copy   

•   Source: SciCrunch Registry

https://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger

Software tool as set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants by 10x Genomics.

Proper citation: Long Ranger (RRID:SCR_018925) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/software/elda/

Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly.

Proper citation: ELDA (RRID:SCR_018933) Copy   

•   Source: SciCrunch Registry

https://github.com/Trinotate/Trinotate.github.io/wiki

Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

Proper citation: Trinotate (RRID:SCR_018930) Copy   

•   Source: SciCrunch Registry

https://open.scayle.es/about

Open source data platform and multidisciplinary online repository where research groups and different organizations store and make public their datasets, managed by Scayle. Collection of public datasets are available through open.scayle.es and can be reused. NetFlow is network protocol developed by Cisco for collection and monitoring of network traffic flow data generated. Netflow datasets have been used to train machine learning models.

Proper citation: Scayle (RRID:SCR_019064) Copy   

•   Source: SciCrunch Registry