Tools   Select Another Resource Report Type

https://github.com/sdorkenw/MeshParty

Software package for working with neuronal meshes, skeletons, and annotations from electron microscopy data. Used to work with meshes, designed around use cases for analyzing neuronal morphology.

Proper citation: MeshParty (RRID:SCR_021873) Copy   

•   Source: SciCrunch Registry

https://github.com/leylabmpi/endoR/

Software R package to interpret fitted tree ensemble model.Used to extract and visualize how predictive variables contribute to tree ensemble model accuracy.

Proper citation: endoR (RRID:SCR_021916) Copy   

•   Source: SciCrunch Registry

https://github.com/wehr-lab/autopilot

Software tool as open source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Toolkit of flexible modules to design experiments without rigid programming and API limitations.

Proper citation: AutoPilot (RRID:SCR_021518) Copy   

•   Source: SciCrunch Registry

https://iopscience.iop.org/article/10.1088/0957-0233/20/10/104035

Software package for advanced time domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data.

Proper citation: jMRUI (RRID:SCR_021893) Copy   

•   Source: SciCrunch Registry

https://github.com/oushujun/EDTA

Software package to filter out false discoveries in raw TE candidates and generate high quality non redundant TE library for whole genome TE annotations.Produces filtered non redundant TE library for annotation of structurally intact and fragmented elements.

Proper citation: EDTA (RRID:SCR_022063) Copy   

•   Source: SciCrunch Registry

https://github.com/jgraving/DeepPoseKit

Software toolkit with high level API for 2D pose estimation of user defined keypoints using deep learning.Written in Python and built using Tensorflow and Keras.Method for pose estimation developed by behavioral scientists at the Max Planck Institute of Animal Behavior.

Proper citation: DeepPoseKit (RRID:SCR_021405) Copy   

•   Source: SciCrunch Registry

https://neurokit2.readthedocs.io/en/latest/

Software Python package for neurophysiological signal processing. Used to analyze physiological data.

Proper citation: Neurokit2 (RRID:SCR_021889) Copy   

•   Source: SciCrunch Registry

https://github.com/DrCoffey/DeepSqueak

Software MATLAB package for high throughput ultrasonic vocalizations detection, classification, and analysis.

Proper citation: DeepSqueak (RRID:SCR_021524) Copy   

•   Source: SciCrunch Registry

https://github.com/ggruenhagen3/coselens

Software R package to detect gene level differential selection between two groups of samples.Used for calculation of excess of non synonymous mutations between two groups.

Proper citation: Coselens (RRID:SCR_022578) Copy   

•   Source: SciCrunch Registry

https://github.com/jokergoo/EnrichedHeatmap

Software R package for comprehensive visualization of genomic signal associations. Visualizes enrichment of genomic signals on specific target regions. Used to visualize e.g. how histone marks are enriched to specific sites.

Proper citation: EnrichedHeatmap (RRID:SCR_023082) Copy   

•   Source: SciCrunch Registry

https://github.com/plaisier-lab/sygnal

Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts.

Proper citation: SYGNAL (RRID:SCR_023080) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=NMF

Software R package for nonnegative matrix factorization. Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms.

Proper citation: Algorithms and Framework for Nonnegative Matrix Factorization (RRID:SCR_023124) Copy   

•   Source: SciCrunch Registry

https://yeatmanlab.github.io/pyAFQ/

Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry.

Proper citation: Automated Fiber Quantification in Python (RRID:SCR_023366) Copy   

•   Source: SciCrunch Registry

https://github.com/Vaa3D/vaa3d_tools/tree/master/hackathon/mBrainAligner

Software package provides cross modality image registration pipeline to support whole brain mapping projects. Contains three modules: (1) image preprocessing and global registration, (2) Coherent Landmark Mapping (CLM) based automatic registration, and (3) optional semi-automatic refinement.

Proper citation: mBrainAligner (RRID:SCR_022791) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/rms/

Software R package as collection of functions that assist with streamline modeling. Works with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.

Proper citation: Regression Modeling Strategies (RRID:SCR_023242) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Maaslin2.html

SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features.

Proper citation: MaAsLin2 (RRID:SCR_023241) Copy   

•   Source: SciCrunch Registry

https://github.com/plger/scDblFinder

Software package for detection and handling of doublets/multiplets in single cell sequencing data.

Proper citation: scDblFinder (RRID:SCR_022700) Copy   

•   Source: SciCrunch Registry

https://ndphillips.github.io/FFTrees/

Software package as decision algorithms for solving binary classification problems. Faster and more frugal because every node allows making decision. Apart from being faster and requiring less information, FFTs tend to be robust against overfitting, and are easy to interpret, use, and communicate.

Proper citation: FFTrees (RRID:SCR_023359) Copy   

•   Source: SciCrunch Registry

https://entap.readthedocs.io/en/latest/

Software package as eukaryotic non model annotation pipeline.Used for bringing functional annotation to non-model eukaryotic transcriptomes to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. Addresses fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates of protein-coding transcripts.

Proper citation: EnTAP (RRID:SCR_023010) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/reshape2/index.html

Software R package to flexible rearrange, reshape and aggregate data. Reshape2 is reboot of reshape package.

Proper citation: reshape2 (RRID:SCR_022679) Copy   

•   Source: SciCrunch Registry