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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
https://github.com/hietakangas-laboratory/LAM
Software Python package for spatially defined cellular phenotyping using image segmentation data from linearizable tissue.Software quantitative phenotyping tool intended for regionally defined analysis of Drosophila midguts based on objects detected from microscopy images.
Proper citation: Linear Analysis of Midgut (RRID:SCR_021255) Copy
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
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
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
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
https://github.com/DrCoffey/DeepSqueak
Software MATLAB package for high throughput ultrasonic vocalizations detection, classification, and analysis.
Proper citation: DeepSqueak (RRID:SCR_021524) Copy
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
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
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
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
https://github.com/PeterEckmann1/preprint-match
Software tool to match bioRxiv preprints with their corresponding PubMed paper.
Proper citation: PreprintMatch (RRID:SCR_022302) Copy
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
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
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
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
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
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
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
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
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