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http://www.drive5.com

Software application that provides search and clustering functionality, typically used with amplicon sequence data. Used to assign sequences to clusters.

Proper citation: USEARCH (RRID:SCR_027438) Copy   

•   Source: SciCrunch Registry

https://www.iqm.unicamp.br/institucional/infraestrutura/cemuiq/liafq/

Laboratory for Physicochemical Analysis of IQ-UNICAMP houses equipment for a range of analytical techniques:Thermal Analysis comprises techniques that measure the physical or chemical properties of a substance, or its reaction products, under controlled temperature variation;Atomic Spectrometry enables multi-element determination in solution samples;Elemental Analysis is used to determine the Carbon, Hydrogen, and Nitrogen content in solid and viscous samples.Nitrogen Physisorption is a technique used to determine the surface area and pore size of solid materials.

Proper citation: State University of Campinas LIAFQ-IQ Laboratory of Physicochemical Analysis Core Facility (RRID:SCR_027389) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/sesame.html

Software R package for reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.

Proper citation: SeSAMe (RRID:SCR_027388) Copy   

•   Source: SciCrunch Registry

https://www.revvity.com/product/ivis-spectrum-2-imaging-system-cls158738

In vivo optical imaging system used in preclinical research to non-invasively monitor and quantify biological processes in living animals over time. Designed with innovative camera with patented coating that delivers high sensitivity 2D and 3D bioluminescence and fluorescence imaging capabilities.

Proper citation: Revvity: IVIS Spectrum 2 In Vivo Imaging System (RRID:SCR_027425) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/transformers/

Software framework for machine learning models in text, computer vision, audio, video, and multimodal model, for both inference and training.

Proper citation: Transformers (RRID:SCR_027381) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/imageio/

Software Python library to read and write wide range of image data, including animated images, volumetric data, and scientific formats. It is cross-platform, runs on Python 3.9+, and is easy to install.

Proper citation: imageio (RRID:SCR_027383) Copy   

•   Source: SciCrunch Registry

https://github.com/jzhang-dev/FEDRANN

Software scalable pipeline for overlap detection based on large-scale sequencing data. It is based on three steps: feature extraction, dimenality reduction, and approximate k-nearest neighbor search. Used for effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.

Proper citation: Fedrann (RRID:SCR_027416) Copy   

•   Source: SciCrunch Registry

https://jaaba.sourceforge.net/

Web application to create variety of automatic behavior classifiers. These classifiers input the animals' trajectories computed by tracking system, and they output time series indicating whether each animal is performing a given behavior in each video frame. Interactive machine learning for automatic annotation of animal behavior. Used to automatically compute interpretable, quantitative statistics describing video of behaving animals.

Proper citation: Janelia Automatic Animal Behavior Annotator (RRID:SCR_027430) Copy   

•   Source: SciCrunch Registry

https://github.com/hejDMC/napari-dmc-brainmap

Software napari plugin for flexible mapping of various features (cell bodies, axonal densities, injections sites, optical fibers, Neuropixels probes) to standardized reference spaces included in BrainGlobe. Used for anatomical mapping.

Proper citation: DMC-BrainMap (RRID:SCR_027433) Copy   

•   Source: SciCrunch Registry

https://github.com/hejDMC/dmc-fluoimager

Software Python project for whole slide image acquisition using a fluorescence microscope.

Proper citation: DMC-FluoImager (RRID:SCR_027435) Copy   

•   Source: SciCrunch Registry

https://github.com/jmschrei/memesuite-lite

Software application as lightweight reimplementation of some of the algorithms in the MEME suite in Python.

Proper citation: memesuite-lite (RRID:SCR_027429) Copy   

•   Source: SciCrunch Registry

https://www.chemdiv.com/

Target-to-Clinic Contract Research Organization (CRO) headquartered in San Diego, CA USA. ChemDiv executes pre-clinical discovery chemistry and biology for drug development and clinical trials for international portfolio of companies across the entire range of targets with small molecule and biotech drugs. The company operates multiple research and development (R&D) subsidiaries in Russia, Ukraine and China as well as business operations around the world.

Proper citation: ChemDiv (RRID:SCR_027402) Copy   

•   Source: SciCrunch Registry

https://www.bruker.com/en/products-and-solutions/mr/nmr/avance-nmr-spectrometer.html

Bruker’s Avance NMR spectrometers are utilized in various scientific fields to elucidate the structure, dynamics, and interactions of molecules. Avance spectrometers are composed of three main hardware components: console, which is the central control unit of the NMR spectrometer, and houses sophisticated electronics for the generation of the pulse sequences and for data acquisition and processing; superconducting magnet to generate homogenous and stable magnetic field to polarize the nuclear spins in the sample; probe for transmitting radiofrequency pulses and detecting the resulting signals from the sample.

Proper citation: Bruker: Avance NMR Spectrometer (RRID:SCR_027378) Copy   

•   Source: SciCrunch Registry

https://github.com/shapely/shapely

Software Python package for manipulation and analysis of geometric objects in the Cartesian plane.

Proper citation: Shapely (RRID:SCR_027411) Copy   

•   Source: SciCrunch Registry

https://github.com/mjskay/ARTool

Software R package for aligned rank transform for nonparametric factorial ANOVAs.

Proper citation: ARTool (RRID:SCR_027412) Copy   

•   Source: SciCrunch Registry

https://cloud.sylabs.io/library/jsaraiva/repo/hvrlocator

Software application to identify spanning hypervariable region(s) from amplicon sequencing variants or SRA public runs (SRR). Aligns query sequences to reference E. coli full-length 16S rRNA gene and identifies spanning region through alignment. Used for identifying hypervariable regions in 16S rRNA big datasets.

Proper citation: HVRLocator (RRID:SCR_027407) Copy   

•   Source: SciCrunch Registry

https://github.com/phipsonlab/speckle

Software R package to analyse differences in cell type proportions in single cell RNA-seq data. Used for analysing single cell data.

Proper citation: speckle (RRID:SCR_027464) Copy   

•   Source: SciCrunch Registry

https://atlas.ctglab.nl/

Updated knowledgebase integrating more curated associations in plants and animals. manually curated resource of genome-wide genotype-to-phenotype associations for a wide range of species. Database of publicly available GWAS summary statistics. Each GWAS can be browsed with the manhattan plot, risk loci, MAGMA (i.e. gene-based) results, SNP heritability and genetic correlations with other GWAS in the database. Full summary statistics can be downloaded from the original source following the provided links.

Proper citation: GWAS Atlas (RRID:SCR_027466) Copy   

•   Source: SciCrunch Registry

https://lightning.ai/

Open-source software Python library that provides high-level interface for PyTorch deep learning framework.

Proper citation: PyTorch Lightning (RRID:SCR_027468) Copy   

•   Source: SciCrunch Registry

https://github.com/wheaton5/souporcell

Software tool to cluster cells using the genetic variants detected within the scRNAseq reads. Robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Used for clustering scRNAseq by genotypes.

Proper citation: Souporcell (RRID:SCR_027462) Copy   

•   Source: SciCrunch Registry