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https://github.com/BioDepot/nbdocker

Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment.

Proper citation: nbdocker (RRID:SCR_017159) Copy   

•   Source: SciCrunch Registry

https://github.com/eegsynth/eegsynth

Open source Python codebase that provides real-time interface between open-hardware devices for electrophysiological recordings like EEG, EMG, and ECG, and analog and digital devices like MIDI, OSC, and analog synthesizers. This allows one to use electrical brain/body activity to flexibly control devices in real-time.

Proper citation: EEGsynth (RRID:SCR_018732) Copy   

•   Source: SciCrunch Registry

http://www.getpaint.net/

Software tool as image and photo editor for PCs that run Windows. Features user interface with support for layers, unlimited undo, special effects, and variety of useful and powerful tools.

Proper citation: paint.net (RRID:SCR_017641) Copy   

•   Source: SciCrunch Registry

https://github.com/pachterlab/kb_python

Software Python package that wraps kallisto and bustools single-cell RNA-seq workflow. Used for single-cell RNA-seq pre-processing. Simplifies downloading and running of kallisto and bustools programs. Consists of kb ref and kb count commands. kb ref builds or downloads species specific index for pseudo alignment of reads and must be run prior to kb count and it runs kallisto index. kb count runs kallisto and bustools programs and is used for pre-processing of data from variety of single-cell RNA-seq technologies, and for number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.).

Proper citation: kb_python (RRID:SCR_018213) Copy   

•   Source: SciCrunch Registry

http://treesoft.sourceforge.net/treebest.shtml

Software package to build, manipulate and display phylogenetic trees. Designed for building gene trees with known species tree and is highly efficient and accurate.

Proper citation: TreeBeST (RRID:SCR_018173) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenMendel/MendelIHT.jl

Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs.

Proper citation: MendelIHT.jl (RRID:SCR_018292) Copy   

•   Source: SciCrunch Registry

https://github.com/smajidian/phaseme

Software tool set to assess quality of per read phasing information and help to reduce errors during this process.

Proper citation: PhaseME (RRID:SCR_018739) Copy   

•   Source: SciCrunch Registry

https://www.acdlabs.com/products/draw_nom/draw/chemsketch/index.php

Software tool as molecular structure drawing application by ACD Labs. Allows user to Draw chemical structures, reactions, and schema, and access variety of graphical tools and templates, Generate names from molecular structure and vice versa, Calculate molecular properties from chemical structure, Create professional reports, presentations, and publication ready figures, Communicate scientific information with clarity and ease.

Proper citation: ACD/ChemSketch (RRID:SCR_019272) Copy   

•   Source: SciCrunch Registry

https://www.biorxiv.org/content/10.1101/2020.09.24.311282v2.full

Software package to quickly transform microscope images into quality figures. User friendly tool for creating and formatting scientific figures, can export files into popular softwares like Adobe Illustrator, Microsoft Powerpoint, and Inkscape.

Proper citation: QuickFigures (RRID:SCR_019082) Copy   

•   Source: SciCrunch Registry

https://www.rankinbiomed.com/product/refurbished-american-optical-860-sliding-micrtome/

THIS REOURCE IS NO LONGER IN SERVICE. Documented on September 29,2023. Sliding microtome used for cutting hard objects such as bone, wood, frozen celloidin, and paraffin preparations. Cutting thickness is adjustable from 1 to 40 microns.

Proper citation: American Optical: 860 Sliding Microtome (RRID:SCR_018434) Copy   

•   Source: SciCrunch Registry

https://github.com/dandi/dandi-cli/

Command line client to facilitate common operations.

Proper citation: dandi-cli (RRID:SCR_019009) Copy   

•   Source: SciCrunch Registry

https://docs.conda.io/en/latest/

Software tool as cross platform, language agnostic binary package manager. Open source package management system and environment management system that runs on Windows, macOS and Linux. Can quickly install, run, and update packages and their dependencies. Package, dependency and environment management for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN, and more. Created for Python programs, but it can package and distribute software for any language. Conda can be combined with continuous integration systems such as Travis CI and AppVeyor to provide frequent, automated testing of your code. Conda package and environment manager is included in all versions of Anaconda and Miniconda.

Proper citation: Conda (RRID:SCR_018317) Copy   

•   Source: SciCrunch Registry

https://bioconda.github.io/

Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install.

Proper citation: BioConda (RRID:SCR_018316) Copy   

•   Source: SciCrunch Registry

https://github.com/benmarwick/cvequality

Software R package contains functions to test for significant differences in coefficients of variation among multiple groups of observations.

Proper citation: cvequality (RRID:SCR_019124) Copy   

•   Source: SciCrunch Registry

https://github.com/ikmb/gwas-qc/

Software tool as scalable GWAS Quality Control pipeline for biobank scale datasets.

Proper citation: GWAS Quality Control Pipeline (RRID:SCR_019241) Copy   

•   Source: SciCrunch Registry

https://bio.tools/galactic_circos

Software tool as Galaxy wrapper providing GUI for Circos tool. Circos allows visualizing data in circular format.

Proper citation: Galactic Circos (RRID:SCR_018207) Copy   

•   Source: SciCrunch Registry

https://github.com/mridulaprasad/CorrDrugTumorMSI

Software R pipeline to correlate drug distribution with tumor tissue types in mass spectrometry imaging data.

Proper citation: CorrDrugTumorMSI (RRID:SCR_018962) Copy   

•   Source: SciCrunch Registry

https://bioinf.shenwei.me/seqkit/

Software tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation.

Proper citation: SeqKit (RRID:SCR_018926) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/jupyter-client/5.2.3/

Jupyter protocol implementation and client libraries. Part of Project Jupyter which exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages. Jupyter-client contains reference implementation of Jupyter protocol and provides client and kernel management APIs for working with kernels.

Proper citation: Jupyter-client (RRID:SCR_018413) Copy   

•   Source: SciCrunch Registry

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

Software R package to run minimum hypergeometric test.

Proper citation: Minimum-Hypergeometric Test (RRID:SCR_018776) Copy   

•   Source: SciCrunch Registry