Tools   Select Another Resource Report Type

https://omictools.com/tiltpicker-tool

Software tool to facilitate particle selection in single particle electron microscopy. An interactive graphical interface application designed to streamline the selection of particle pairs from tilted-pair datasets. Designed to work with existing software tools for image processing.

Proper citation: TiltPicker (RRID:SCR_016674) Copy   

•   Source: SciCrunch Registry

http://spark.apache.org/

Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework.

Proper citation: Apache Spark (RRID:SCR_016557) Copy   

•   Source: SciCrunch Registry

https://github.com/kendomaniac/docker4seq

Software R package to execute next generation sequencing computing applications, e.g. reads mapping and counting, wrapped in docker containers.

Proper citation: docker4seq (RRID:SCR_017006) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenGene/AfterQC

Software that performs automatic filtering, trimming, error removing, and quality control for fastq data.

Proper citation: AfterQC (RRID:SCR_016390) Copy   

•   Source: SciCrunch Registry

https://github.com/facebook/prophet

Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton.

Proper citation: Prophet (RRID:SCR_017083) Copy   

•   Source: SciCrunch Registry

http://databiosphere.org

Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations.

Proper citation: Data Biosphere (RRID:SCR_016154) Copy   

•   Source: SciCrunch Registry

http://regent.qc.ca/assets/winrhizo_software.html

Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots.

Proper citation: WinRHIZO (RRID:SCR_017120) Copy   

•   Source: SciCrunch Registry

http://www.ccp4.ac.uk/html/aimless.html

Data processing software for x-ray diffraction data. AIMLESS scales together multiple observations of reflections, and merges multiple observations into an average intensity.

Proper citation: AIMLESS (RRID:SCR_015747) Copy   

•   Source: SciCrunch Registry

https://www.globalphasing.com/autoproc/

Data processing software for X-ray diffraction data. autoPROC is a set of tools and programs to automate steps involved in data processing, such as image analysis, integration, indexing, and determination.

Proper citation: autoPROC (RRID:SCR_015748) Copy   

•   Source: SciCrunch Registry

https://stfc.ukri.org/

One of nine Councils within United Kingdom Research and Innovation, an organisation that brings together the UK’s Research Councils, Innovate UK and Research England. Works in partnership with universities, research organisations, businesses, charities, and government to create the environment for research and innovation.

Proper citation: Science and Technology Facilities Council (RRID:SCR_016713) Copy   

•   Source: SciCrunch Registry

http://reproducibility.stanford.edu/

Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects.

Proper citation: Stanford Center for Reproducible Neuroscience (RRID:SCR_016684) Copy   

•   Source: SciCrunch Registry

https://github.com/TeamMacLean/atacr

Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes.

Proper citation: atacr (RRID:SCR_016286) Copy   

•   Source: SciCrunch Registry

http://www.studylog.com

Commerciall organization to develop study protocols collaboratively to run and manage animal research studies for academic, government, biotech and pharmaceutical labs. Provides services, including product installation and configuration, user training, customization services and ongoing support.

Proper citation: Studylog (RRID:SCR_016682) Copy   

•   Source: SciCrunch Registry

https://github.com/kstreet13/slingshot

Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics.

Proper citation: Slingshot (RRID:SCR_017012) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

https://github.com/BodenmillerGroup/imctools

Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc.

Proper citation: imctools (RRID:SCR_017132) Copy   

•   Source: SciCrunch Registry

https://github.com/neuropoly/qMRLab

Software for quantitative MR image analysis, simulation, and protocol optimization. It aims to provide the community with a tool for data fitting, plotting, simulation and protocol optimization for a variety of different quantitative models.

Proper citation: qMRLab (RRID:SCR_016256) Copy   

•   Source: SciCrunch Registry

https://github.com/colinvaz/nmf-toolbox

Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach.

Proper citation: NMF Toolbox (RRID:SCR_017069) Copy   

•   Source: SciCrunch Registry

http://www.usccn.org/Pages/default.aspx

Research coordination network for ex situ Microbial Germplasm Collections to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of humankind by providing opportunities for US culture collection workers to engage with each other and with the broader culture collection community.

Proper citation: U.S. Culture Collection Network (USCCN) (RRID:SCR_016777) Copy   

•   Source: SciCrunch Registry

http://www.viagenbiotech.com

Commercial provider of innovative DNA extraction technologies and products for life science research. Reagents for preparation of DNA from mouse tails, ear pieces, yolk sac, and culture cells, DNA extracts, DNA markers.

Proper citation: Viagen Biotech (RRID:SCR_017106) Copy   

•   Source: SciCrunch Registry

https://sils.fnwi.uva.nl/bcb/Object-Image/object-image.html

Image analysis software package that allows non-destructive image marking, input for further image processing, and marking the results of automatic measurements. Object-Image integrates measurements, macros, graphical objects and image names in a closed unit called 'object file' so that it reduces file clutter.

Proper citation: Object-Image (RRID:SCR_015720) Copy   

•   Source: SciCrunch Registry