Tools   Select Another Resource Report Type

https://github.com/MMTI/Toolkit_for_MIRA_LAB_Striatal_Segmentation

Software MATLAB pipeline that produces CNN-based segmentations of striatal regions of brain based on structural T1w image.

Proper citation: Toolkit for MIRA LAB Striatal Segmentation (RRID:SCR_023073) Copy   

•   Source: SciCrunch Registry

https://github.com/ParkerLab/ataqv

Software package for QC and visualization of ATAC-seq results. Used to examine aligned reads and report basic metrics, including reads mapped in proper pairs, optical or PCR duplicates, reads mapping to autosomal or mitochondrial references, ratio of short to mononucleosomal fragment counts, mapping quality, various kinds of problematic alignments.

Proper citation: ataqv (RRID:SCR_023112) Copy   

•   Source: SciCrunch Registry

https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revao_14dec2018

Software toolkit that enables real-time basecalling and several post-processing features that works on Oxford Nanopore Technologies sequencing platforms. Data processing toolkit that contains Oxford Nanopore Technologies basecalling algorithms, and several bioinformatic post-processing features. Provided as binaries to run on Windows, OS X and Linux platforms, as well as being integrated with MinKNOW, Oxford Nanopore device control software.

Proper citation: Guppy basecaller (RRID:SCR_023196) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://drawio-app.com/product/

Software tool as diagramming application that enables collaboration in real time.

Proper citation: draw.io (RRID:SCR_022939) Copy   

•   Source: SciCrunch Registry

https://github.com/sapporo-wes/sapporo-service

Software for standard implementation conforming to Global Alliance for Genomics and Health Workflow Execution Service API specification.

Proper citation: Sapporo service (RRID:SCR_023202) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/de/de/home/digital-science/thermo-fisher-connect.html

Platform for connecting people, software, data, and equipment. Helps integrating software, instruments, and data across your lab’s existing ecosystem. Provides: workflows guide users through processes involving multiple systems;Centralized access to Thermo Fisher Scientific instrument service and expertise;Connectivity to monitor and maintain instruments and equipment;Granular data sharing controls to enhance collaboration;Secure environment.

Proper citation: ThermoFisher Connect Platform (RRID:SCR_023441) Copy   

•   Source: SciCrunch Registry

https://hla-net.eu/tools/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://pypi.org/project/findmaxima2d/

Software Python 2D Maxima finding algorithm. Re-implementation of Java plugin for ImageJ/Fiji.

Proper citation: findmaxima2d (RRID:SCR_023332) Copy   

•   Source: SciCrunch Registry

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

Software R package to read, write, manipulate and analyze variant call format data. Facilitates easy manipulation of variant call format (VCF) data.

Proper citation: vcfR (RRID:SCR_023453) Copy   

•   Source: SciCrunch Registry

https://grunwaldlab.github.io/poppr/

Software R package for analysis of populations with mixed modes of sexual and clonal reproduction. Used for genetic analysis of populations with mixed reproduction.

Proper citation: poppr (RRID:SCR_023452) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.google.com/intl/de/forms/about/

Software for creating surveys and questionnaires.

Proper citation: Google Forms (RRID:SCR_023174) Copy   

•   Source: SciCrunch Registry

https://github.com/sapporo-wes/tonkaz

Software CLI tool to verify workflow reproducibility.

Proper citation: Tonkaz (RRID:SCR_023206) Copy   

•   Source: SciCrunch Registry

https://github.com/fritzsedlazeck/SURVIVOR

Software tool set for simulating and evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs. Used for for SV simulation, comparison and filtering.

Proper citation: SURVIVOR (RRID:SCR_022995) Copy   

•   Source: SciCrunch Registry