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https://github.com/jkimlab/PLR-GEN
Software package for generation of pseudo long reads by using short reads of metagenomic sample and microbial reference genome sequences as input.
Proper citation: PLR-GEN (RRID:SCR_022264) Copy
https://stringr.tidyverse.org/
Software package to provide set of functions designed to make working with strings easy. Consistent wrappers for common string operations.
Proper citation: stringr (RRID:SCR_022813) Copy
https://www.oracle.com/applications/crystalball/
Software spreadsheet based application for risk measurement and reporting, Monte Carlo simulation, time series forecasting, and optimization.Provides realistic and accessible way of modeling uncertainty, enabling you to measure and report on risk inherent in your key metrics.
Proper citation: Oracle Crystal Ball (RRID:SCR_023226) Copy
https://github.com/lapphe/raspberry_rat
Software Python platform for recording, converting, and uploading videos to cloud and for performing scheduled video recordings. Repository also includes wiki section with comprehensive guide to setting up Raspberry Pis for this purpose. Raspberry Pis are often cheaper than camcorder and can produce HD video. They are also equipped with infrared camera, making them ideal for recordings of animals that are active in low light conditions.
Proper citation: Rasberry rat (RRID:SCR_023467) Copy
Software cross platform mobile application that supports 2D/3D/4D image visualization, multi-morphometry annotation, proofreading, interactive imaging system controlling, and distributed collaboration.
Proper citation: Hi5App (RRID:SCR_022819) Copy
https://drawio-app.com/product/
Software tool as diagramming application that enables collaboration in real time.
Proper citation: draw.io (RRID:SCR_022939) Copy
https://github.com/replikation/What_the_Phage
Parallel multitool approach for phage prediction combined with annotation and classification downstream strategy. Used for identification and analysis of phage sequences. Phage identification via nextflow and docker or singularity.
Proper citation: What the Phage (RRID:SCR_022871) Copy
https://www.jmp.com/en_us/home.html
Statistical software tool. Predictive analytics software. Offers all tools in JMP plus advanced features for more sophisticated analyses.
Proper citation: SAS JMP Pro (RRID:SCR_022199) Copy
Software pipeline for effective HLA data analysis and its application to 145 population samples from Europe and neighbouring areas. Tools for handling and analysing data with ambiquities.
Proper citation: Generate tools (RRID:SCR_023042) Copy
https://github.com/lambdaloop/anipose
Software package for 3D pose estimation. Uses DeepLabCut for 2D tracking and uses triangulation methods to project pose estimations into three dimensions.Toolkit for robust markerless 3D pose estimation.
Proper citation: Anipose (RRID:SCR_023041) Copy
https://github.com/SydneyBioX/SurvBenchmark_package
Software package for comprehensive benchmarking study of survival analysis methods using both omics data and clinical data. Evaluates diverse collection of survival models for both clinical and omics datasets.
Proper citation: SurvBenchmark (RRID:SCR_022503) Copy
https://github.com/jfarek/xatlas
Software tool as variant caller for SNVs and small indels. Implemented as software application written in C++ .
Proper citation: xAtlas (RRID:SCR_022987) Copy
https://www.starrlifesciences.com/product/small-animal-pulse-oximeter/
Software is part of MouseOx Plus pulse oximeter system.
Proper citation: Starr Life Sciences MouseOx Plus (RRID:SCR_022984) Copy
https://github.com/helioalexandre/MouBeAT
Software package to analyze different behavioral tests in rodents semi-automatically. These tests include Open Field (OF), Elevated Plus Maze (EPM), Y-maze (YM) test and Morris Water Maze (MWM).
Proper citation: Mouse Behavioral Analysis Toolbox (RRID:SCR_023291) Copy
https://github.com/h2oai/h2o4gpu
Interface to H2O4GPU, collection of GPU solvers for machine learning algorithms.
Proper citation: h2o4gpu (RRID:SCR_022520) Copy
https://CRAN.R-project.org/package=irrCAC
Software R package to calculate various chance-corrected agreement coefficients among 2 or more raters. Among CAC coefficients covered are Cohen's kappa, Conger's kappa, Fleiss' kappa, Brennan-Prediger coefficient, Gwet's AC1/AC2 coefficients, and Krippendorff's alpha. Multiple sets of weights are proposed for computing weighted analyses.
Proper citation: Computing Chance Corrected Agreement Coefficients (RRID:SCR_023176) Copy
https://CRAN.R-project.org/package=irrICC
Software R package to calculate various intraclass correlation coefficients. Used to quantify inter-rater and intra-rater reliability.
Proper citation: Intraclass Correlations for Quantifying Inter Rater Reliability (RRID:SCR_023175) Copy
https://www.google.com/intl/de/forms/about/
Software for creating surveys and questionnaires.
Proper citation: Google Forms (RRID:SCR_023174) Copy
https://CRAN.R-project.org/package=shinythemes
Software R package Themes for use with Shiny.
Proper citation: shinythemes (RRID:SCR_022757) Copy
https://github.com/BGI-shenzhen/VCF2Dis
Software to calculate p-distance matrix based Variant Call Format.
Proper citation: VCF2Dis (RRID:SCR_022513) Copy
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