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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://bioconductor.org/packages/karyoploteR/
Software R package used to karyoplots. Bioconductor package to plot customizable genomes displaying arbitrary data.
Proper citation: karyoploteR (RRID:SCR_021824) Copy
https://github.com/NollmannLab/qudi-HiM
Software package for control of optical microscope setups with different hardware components optimized to perform multiplexed imaging experiments. Modular laboratory experiment management suite.
Proper citation: qudi-HiM (RRID:SCR_022114) Copy
https://github.com/sqjin/CellChat
Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.
Proper citation: CellChat (RRID:SCR_021946) Copy
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
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
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
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