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https://cole-trapnell-lab.github.io/monocle3/

Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points.

Proper citation: Monocle3 (RRID:SCR_018685) Copy   

•   Source: SciCrunch Registry

https://www.nikonmetrology.com/en-us/product/az100-multizoom

Nikon Instruments AZ100 C1si is macro confocal microscope system combining stereo and compound microscopes into single hybrid imaging system for dynamic imaging of single cells or whole specimens.System covers range of magnifications from 5x to 400x. Has triple nosepiece that can switch magnifications. AZ100 C1si boasts simultaneous 32 channel spectral image acquisition over spectral range of 320 nm in single scan. Simultaneous 32 channel acquisition at 10 nm, 5 nm or 2.5 nm bandwidths, all software controlled, is possible.

Proper citation: Nikon: AZ100 Confocal Microscope (RRID:SCR_018603) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/microfileplus

Software tool as microscopy image file format converter by MBF Bioscience. Converts common microscopy image files to JPEG2000 and OME-TIFF. Used to view, analyze, and share big image data from many sources.

Proper citation: MicroFilePlus (RRID:SCR_018724) Copy   

•   Source: SciCrunch Registry

https://www.marshallscientific.com/The-MJ-Research-PTC-100-Thermal-Cycler-p/mj-100.htm

Thermocycler that operates with 96 well and 60 well microplates. Has temperature configurations from 0 C to 105 C and pressure and height adjustment via thumbwheel. Comes with 14 pre-programmed protocols.

Proper citation: Marshall Scientific: MJ Research PTC-100 PCR Thermocycler (RRID:SCR_018602) Copy   

•   Source: SciCrunch Registry

https://www.labx.com/product/waters-2695

High performance liquid chromatographic system with quaternary, low pressure mixing pump and inline vacuum degassing. It has wavelengths of 190 to 800 nm and flow rates from 50 uL per min to 5 mL per min with 2.1 mm ID columns and larger. Autosampler has maximum capacity of 120 vials (12x32, 2 mL) with programmable temperature control from 4 to 40C. Heated column compartment provides temperatures from 5 degrees above ambient to 65C.

Proper citation: Waters: 2695 HPLC System (RRID:SCR_018649) Copy   

•   Source: SciCrunch Registry

https://www.bpforms.org

Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts.

Proper citation: BpForms (RRID:SCR_018653) Copy   

•   Source: SciCrunch Registry

https://www.objtables.org

Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort.

Proper citation: ObjTables (RRID:SCR_018652) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=trend

Software package includes tests for trends and change points detection. Used in analysis of environmental data.

Proper citation: trend (RRID:SCR_018658) Copy   

•   Source: SciCrunch Registry

https://www.nexcelom.com/nexcelom-products/cellometer-fluorescent-viability-cell-counters/cellometer-auto-2000/

Cell viability counter. Touchscreen fluorescent automated cell counter for primary samples by Nexcelom Bioscience.

Proper citation: McKinley: Cellometer Auto 2000 Cell Viability Counter (RRID:SCR_018656) Copy   

•   Source: SciCrunch Registry

https://hartleys.github.io/QoRTs/

Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R.

Proper citation: QoRTs (RRID:SCR_018665) Copy   

•   Source: SciCrunch Registry

http://smithlabresearch.org/software/preseq/

Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries.

Proper citation: Preseq (RRID:SCR_018664) Copy   

•   Source: SciCrunch Registry

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

HFX offers scanning rate to improve proteomic depth for discovery applications. Integrates well with targeted applications such as parallel reaction monitoring. Mass Spectrometer to identify and quantify proteins, peptides, lipids, glycans and small molecules accurately.

Proper citation: Thermo Fisher: QE-HFX mass spectrometer (RRID:SCR_018703) Copy   

•   Source: SciCrunch Registry

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

System includes Thermo Orbitrap Fusion Tribrid mass spectrometer and Waters M-Class Acquity nanoUPLC. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments.

Proper citation: Thermo Fisher: Orbitrap Fusion nanoLC/MS system (RRID:SCR_018702) Copy   

•   Source: SciCrunch Registry

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

LTQ XL ion trap mass spectrometer with Agilent 1100 HPLC system for metabolite identification, stability testing, degradation products, and high abundance quantitation.

Proper citation: Thermo Fisher: LTQ XL LC/MS system (RRID:SCR_018701) Copy   

•   Source: SciCrunch Registry

https://github.com/wangdingkang/DiscreteMorse

Discrete Morse based pipeline for neuron tracing on tracer injection and single neuron data sets. Automatically generates set of trees summarization of given neuron imaging data. Used to extract tree skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections.

Proper citation: Discrete Morse (RRID:SCR_018662) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/minet/

Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data.

Proper citation: minet (RRID:SCR_018661) Copy   

•   Source: SciCrunch Registry

https://mygene.info/

Web service for querying or retrieving gene annotation data.

Proper citation: MyGene.info (RRID:SCR_018660) Copy   

•   Source: SciCrunch Registry

https://www.mpbio.com/fastprep-24-5g-instrument

Sample disruption instrument that can homogenize, grind, or lyse biological samples. Samples are added to individual lysing matrix tubes and shaken in tridimensional motion.

Proper citation: MP Biochemicals: FastPrep24 Sample Preparation (RRID:SCR_018599) Copy   

•   Source: SciCrunch Registry

http://labx.com/product/stratagene-stratalinker-1800

UV crosslinker designed to crosslink DNA or RNA to nylon, nitrocellulose, or nylon reinforced nitrocellulose membranes in 25 to 50 seconds. It is equipped with internal photodetector to compensate for aging ultraviolet bulbs.

Proper citation: Stratagene: 1800 UV Crosslinker (RRID:SCR_018631) Copy   

•   Source: SciCrunch Registry

https://www.labx.com/product/sciex-4000-qtrap-

Hybrid triple quadrupole linear ion trap mass spectrometer for drug discovery and development, metabolite identification, contaminant testing, proteomic applications, post translationally modified proteins discovery, protein identification, and biomarker validation.

Proper citation: SCIEX: 4000 QTRAP Mass Spectrometer (RRID:SCR_018630) Copy   

•   Source: SciCrunch Registry