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http://cran.r-project.org/web/packages/CpGassoc/index.html

Software R package to test association between methylation at CpG sites across genome and phenotype of interest, adjusting for any relevant covariates. Can perform standard analyses of large datasets without need to manually input data. Can handle mixed effects models with chip or batch entering model as random intercept. Includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.

Proper citation: CpGassoc (RRID:SCR_000320) Copy   

•   Source: SciCrunch Registry

https://www.ucpress.edu/

Publishing house associated with University of California that engages in academic publishing. UC Press Foundation raises funds to uphold vital role as independent, nonprofit publisher, and receives philanthropic support.

Proper citation: University of California Press (RRID:SCR_024647) Copy   

•   Source: SciCrunch Registry

https://www.leica-microsystems.com/products/confocal-microscopes/p/stellaris-8-falcon/

Microscope for functional imaging. Used to investigate cellular physiology and to explore dynamics in living cells. Enables video rate lifetime imaging acquisition for rapid kinetic studies in live cells. Adds new dimension of contrast to imaging for biosensing and tracking of interactions between proteins.

Proper citation: Leica: STELLARIS 8 FALCON FLIM microscope (RRID:SCR_024660) Copy   

•   Source: SciCrunch Registry

https://www.leica-microsystems.com/products/confocal-microscopes/p/stellaris-8-crs/

Microscope enables to implement label free chemical imaging. Used to study structures that cannot be visualized with traditional fluorescent microscopy methods.

Proper citation: Leica: STELLARIS 8 CRS microscope (RRID:SCR_024661) Copy   

•   Source: SciCrunch Registry

https://www.leica-microsystems.com/products/confocal-microscopes/p/stellaris-8/

STELLARIS 5 microscope has core system with integrated WLL, combined with proprietary Acousto-Optical Beam Splitter and Power HyD S detectors. Together with the TauSense technology, STELLARIS 5 sets a new standard for the quality of images and quantity of information generated. Imaging with user interface, ImageCompass.

Proper citation: Leica: STELLARIS 5 microscope (RRID:SCR_024663) Copy   

•   Source: SciCrunch Registry

https://www.leica-microsystems.com/products/confocal-microscopes/p/stellaris-8/

STELLARIS 8 microscope with core system addition of spectrum WLL and specialized detector options of Power HyD family to expand range of confocal applications. Can be combined with all Leica Microsystems modalities, including FAst Lifetime CONtrast (FALCON), Deep In Vivo Explorer (DIVE), STED, Digital Light Sheet (DLS) and CARS. STELLARIS 8 new features maximize the potential of these modalities.

Proper citation: Leica: STELLARIS 8 microscope (RRID:SCR_024664) Copy   

•   Source: SciCrunch Registry

https://www.leica-microsystems.com/products/light-microscopes/p/leica-lmd7/

Laser Microdissection system enables users to isolate specific single cells or entire areas of tissue. Powered by unique laser design and dynamic software, Leica LMD systems allow users to easily isolate Regions of Interest from entire areas of tissue down to single cells or even subcellular structures such as chromosomes. LMD7 provides higher laser power. Suited to dissect any kind of tissue independent of its size or shape.

Proper citation: Leica: LMD7 Laser Microdissection microscope (RRID:SCR_024657) Copy   

•   Source: SciCrunch Registry

https://www.leica-microsystems.com/products/light-microscopes/p/leica-lmd7/

Laser Microdissection system enables users to isolate specific single cells or entire areas of tissue. Powered by unique laser design and dynamic software, Leica LMD systems allow users to easily isolate Regions of Interest from entire areas of tissue down to single cells or even subcellular structures such as chromosomes. Leica LMD6 is for standard tissue dissection. Used for standard applications dissecting soft tissues such as brain, liver, or kidney.

Proper citation: Leica: LMD6 Laser Microdissection microscope (RRID:SCR_024658) Copy   

•   Source: SciCrunch Registry

https://webprotege.stanford.edu

Web based platform for editing biomedical ontologies. Web application for editing OWL 2 ontologies. Open source, lightweight, web based ontology editor implemented in Java and JavaScript using OWL API and Google Web Toolkit. For users who do not wish to host their ontologies on Stanford servers, WebProtégé is available as Web app that can be run locally using Servlet container such as Tomcat.

Proper citation: WebProtege (RRID:SCR_024627) Copy   

•   Source: SciCrunch Registry

https://p2sl.berkeley.edu/about/

Research institute dedicated to developing and deploying knowledge and tools for project management. Projects are temporary production systems. Dedicated to developing and deploying knowledge and tools for management of project production systems and the management of organizations that produce and deliver goods and services through such systems.

Proper citation: Project Production Systems Laboratory (RRID:SCR_024641) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-EUtilities

Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic.

Proper citation: Bio-EUtilities (RRID:SCR_024064) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Tools-Run-Alignment-Clustalw

Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program.

Proper citation: Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Tools-Phylo-PAML

Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output.

Proper citation: Bio-Tools-Phylo-PAML (RRID:SCR_024069) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Graphics

Software package to generate GD images of Bio::Seq objects.

Proper citation: Bio-Graphics (RRID:SCR_024061) Copy   

•   Source: SciCrunch Registry

https://github.com/genouest/biomaj-cli

Software package to use BioMAJ providing biomaj-cli.

Proper citation: CLI for BioMAJ (RRID:SCR_023980) Copy   

•   Source: SciCrunch Registry

https://github.com/dutilh/CAT

Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies.

Proper citation: CAT and BAT (RRID:SCR_023988) Copy   

•   Source: SciCrunch Registry

https://github.com/mroosmalen/nanosv

Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

Proper citation: NanoSV (RRID:SCR_024127) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-ut/GenomeTester4

Software toolkit for performing set operations - union, intersection and complement on k-mer lists.

Proper citation: GenomeTester4 (RRID:SCR_024026) Copy   

•   Source: SciCrunch Registry

https://github.com/nextstrain/augur

Software package to track evolution from sequence and serological data. Provides collection of commands which are designed to be composable into larger processing pipelines.

Proper citation: Augur (RRID:SCR_023964) Copy   

•   Source: SciCrunch Registry

https://cme.h-its.org/exelixis/web/software/exabayes/

Software package for Bayesian tree inference. Used for large-scale analyses on computer clusters.

Proper citation: ExaBayes (RRID:SCR_024019) Copy   

•   Source: SciCrunch Registry