Tools   Select Another Resource Report Type

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://knowledge.brain-map.org/celltypes

Software application to examine multimodal data from thousands of cells across 3 mammalian species.

Proper citation: Cell Type Knowledge Explorer (RRID:SCR_022793) 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://www.millisecond.com/download/

Software tool for designing and administering psychological tests and experiments on computers.

Proper citation: Inquisit LAB (RRID:SCR_022151) 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://github.com/PeterEckmann1/preprint-match

Software tool to match bioRxiv preprints with their corresponding PubMed paper.

Proper citation: PreprintMatch (RRID:SCR_022302) Copy   

•   Source: SciCrunch Registry

http://www.cgmartini.nl/index.php/downloads/tools/239-insane

Software tool for generating custom membranes for molecular simulations. Software Python script to setup Martini bilayer systems.

Proper citation: insane.py (RRID:SCR_022317) 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

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

Software R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.

Proper citation: Peptides (RRID:SCR_022675) Copy   

•   Source: SciCrunch Registry

https://www.cbcb.umd.edu/software/epiviz

Software package as interactive visualization tool for functional genomics data. Interactive visual analytics for functional genomics data.

Proper citation: Epiviz (RRID:SCR_022796) Copy   

•   Source: SciCrunch Registry

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

Software R package to create tidy data frames of marginal effects for ggplot from model outputs. Used to compute marginal effects and adjusted predictions from statistical models and returns result as tidy data frames.

Proper citation: ggeffects (RRID:SCR_022496) Copy   

•   Source: SciCrunch Registry

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

Software R package for modeling beta distributed dependent variables, e.g., rates and proportions. In addition to maximum likelihood regression (for both mean and precision of beta distributed response), bias corrected and bias reduced estimation as well as finite mixture models and recursive partitioning for beta regressions are provided.

Proper citation: Betareg (RRID:SCR_022494) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/monaLisa/

Software R package to work with sequence motifs in analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of obtained results are also provided.

Proper citation: monaLisa (RRID:SCR_022802) Copy   

•   Source: SciCrunch Registry

https://github.com/shooshtarilab/TMExplorer

Software package to improve studying tumour microenvironment with single cell sequencing. Developers may use this package to obtain data for validation of new algorithms and researchers interested in tumour microenvironment may use it to study specific cancers more closely. Curated collection of scRNAseq datasets sequenced from tumours.

Proper citation: TMExplorer (RRID:SCR_022768) Copy   

•   Source: SciCrunch Registry

https://spin.niddk.nih.gov/bax/software/TALOS-N/

Software package for prediction of protein backbone and sidechain torsion angles from NMR chemical shifts.

Proper citation: TALOS-N (RRID:SCR_022800) Copy   

•   Source: SciCrunch Registry

https://github.com/topepo/caret

Software R package that contains functions for training and plotting classification and regression models. Includes methods for pre-processing training data, calculating variable importance, and model visualizations.

Proper citation: Classification And Regression Training (RRID:SCR_022524) Copy   

•   Source: SciCrunch Registry

https://plexon.com/software-downloads/

Software tool used to control Plexon pattern generator for optogenetic stimulation.

Proper citation: Radiant (RRID:SCR_022645) Copy   

•   Source: SciCrunch Registry

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

Software R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in wide range of genetic architectures, including additive, dominance and epistatic models. Used to simulate multiple traits controlled by loci with varying degrees of pleiotropy.

Proper citation: simplePHENOTYPES (RRID:SCR_022523) Copy   

•   Source: SciCrunch Registry