Tools   Select Another Resource Report Type

http://paintmychromosomes.com/

Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data.

Proper citation: fineSTRUCTURE (RRID:SCR_018170) Copy   

•   Source: SciCrunch Registry

https://servicesn.mbi.ucla.edu/SAVES/

Web server for structure validation in homology modeling. Used to validate of obtained crude models. Structure analysis and validation server.

Proper citation: SAVES (RRID:SCR_018219) Copy   

•   Source: SciCrunch Registry

https://github.com/lmcinnes/umap

Software package as dimension reduction technique that can be used for visualization similar to t-SNE, but also for general non-linear dimension reduction. Used for dimensionality reduction for visualizing single-cell data.

Proper citation: Umap (RRID:SCR_018217) Copy   

•   Source: SciCrunch Registry

https://github.com/yousra291987/ChiCMaxima

Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling.

Proper citation: ChiCMaxima (RRID:SCR_018178) Copy   

•   Source: SciCrunch Registry

https://github.com/esctrionsit/snphub

Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data.

Proper citation: SnpHub (RRID:SCR_018177) Copy   

•   Source: SciCrunch Registry

https://github.com/BUStools/bustools/

Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks.

Proper citation: Bustools (RRID:SCR_018210) Copy   

•   Source: SciCrunch Registry

https://github.com/santeripuranen/SpydrPick

Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree.

Proper citation: SpydrPick (RRID:SCR_018176) Copy   

•   Source: SciCrunch Registry

https://github.com/santeripuranen/SuperDCA

Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis.

Proper citation: SuperDCA (RRID:SCR_018175) Copy   

•   Source: SciCrunch Registry

https://satijalab.org/howmanycells

Web tool for calculating number of cells that must be sampled in order to see at least n cells of each type for single cell genomics experiments.

Proper citation: How many cells (RRID:SCR_018184) Copy   

•   Source: SciCrunch Registry

https://discover.blackfynn.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. Data repository for scientific data. Open data library to explore neuroscience data for neurodegenerative diseases for which there are no disease modifying treatments.

Proper citation: Blackfynn Discover (RRID:SCR_018068) Copy   

•   Source: SciCrunch Registry

https://biospherix.com/products/c-chamber

Culture chamber for cell culture by BioSpherix. Functionalized by gas controllers for all bioactive gases, e.g. O2, CO2, CO, NO, etc. Made of clear polycarbonate. Magnetic seal door. Temperature is controlled. Combines with ProOx 110, ProCO2, ProOx C21, OxyCycler Series.

Proper citation: BioSpherix: C-Chamber (RRID:SCR_018189) Copy   

•   Source: SciCrunch Registry

https://www.medrxiv.org

Free online archive and distribution server for complete but unpublished manuscripts in the medical, clinical, and related health sciences. Preprints are preliminary reports of work that have not been certified by peer review. They should not be relied on to guide clinical practice or health related behavior and should not be reported in news media as established information. Research articles, systematic reviews and meta analyses, clinical research design protocols and data articles may be posted.

Proper citation: medRxiv (RRID:SCR_018222) Copy   

•   Source: SciCrunch Registry

http://www.innovision-systems.com/Products/MaxTraq.html

Software package for motion capture analysis by Innovision Systems Inc.

Proper citation: MaxTRAQ (RRID:SCR_018188) Copy   

•   Source: SciCrunch Registry

https://www.sonybiotechnology.com/us/instruments/sh800s-cell-sorter/

Benchtop cell sorter that sorts wide range of cell sizes for many applications using microfluidic sorting chips. Integrated with comprehensive fluidics controls and advanced automation for set-up, acquisition, sort and analysis. System software supports sorting into tubes and 96- and 384-well plates. Software generates FCS 3.0 and FCS 3.1 files that can be exported to third party analysis tools. For non-clinical research use only. For applications in which cross-contamination is concern, optional e-beam sterilized consumables can be used to replace sample line and sorting chip. Optional class A2 Level II biosafety cabinet provides protection for personnel and products. Biosafety cabinet meets international standards.Optical design offers up to four collinear excitation lasers (488 nm, 405nm, 561nm and 638nm) and six fluorescence detectors. The six free-form PMTs enable detection of fluorescence signals from any laser based on filter selection.

Proper citation: Sony biotechnology: SH800S Cell Sorter (RRID:SCR_018066) Copy   

•   Source: SciCrunch Registry

http://crispr.dbcls.jp/

Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast.

Proper citation: CRISPRdirect (RRID:SCR_018186) Copy   

•   Source: SciCrunch Registry

http://viewer.shigen.info/medakavw/crisprtool/

Web medaka pattern match tool for short sequence and/or pattern. Used to search database of medaka genome on target and off target sites when editing genome with CRISRP-Cas9.

Proper citation: NBRP Medaka Pattern Match (RRID:SCR_018157) Copy   

•   Source: SciCrunch Registry

https://www.mizarimaging.com/wp-content/uploads/2018/11/Tilt-Datasheet-3.pdf

Modular light sheet illumination system designed to image living samples with minimal photobleaching or phototoxicity by Mizar Imaging. Enables high spatial and temporal resolution light sheet imaging to be added to existing or new microscope system.

Proper citation: Mizar Imaging: Tilt High Resolution Light Sheet Imaging System (RRID:SCR_018156) Copy   

•   Source: SciCrunch Registry

https://s2genomics.com/singulator-100/

Singulator to automate tissue preparation for single cell and single nucleus analyses. Bench top Singulator System and single use cartridge enable tissue dissociations into singulated cells or nuclei suspensions.

Proper citation: S2 Genomics: Singulator 100 Automated Single Cell Prep Automated System (RRID:SCR_018155) Copy   

•   Source: SciCrunch Registry

https://www.yxlon.de/en/products/x-ray-and-ct-inspection-systems/yxlon-ff35-ct

Computed tomography system designed to achieve precise inspection results for wide range of applications by YXLON. Available in single or dual tube configuration, it is perfect for very small to medium sized parts inspection in automotive, electronics, aviation, and material science industries.

Proper citation: YXLON: FF35 CT (RRID:SCR_018208) Copy   

•   Source: SciCrunch Registry

http://stmichaelshospitalresearch.ca/wp-content/uploads/2015/09/ZEN-Black-Quick-Guide.pdf

Software used to analyze images obtained from microscope. ZEN Black is software Zeiss uses to run their laser-based instruments.

Proper citation: Black Zen software (RRID:SCR_018163) Copy   

•   Source: SciCrunch Registry