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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://bbknn.readthedocs.io/en/latest/

Software to identify each cell’s top neighbours in each batch separately instead of entire cell pool with no accounting for batch. Nearest neighbours for each batch are then merged to create final list of neighbours for cell. Aligns batches in a quick and lightweight manner.

Proper citation: BBKNN (RRID:SCR_022807) Copy   

•   Source: SciCrunch Registry

https://github.com/wtsi-hpag/PretextView

Software tool to enable visualization from PretextMap output. Desktop application for viewing pretext contact maps. OpenGL Powered Pretext Contact Map Viewer.

Proper citation: PretextView (RRID:SCR_022024) Copy   

•   Source: SciCrunch Registry

https://www.freecad.org/

Open source parametric 3D modeler to design real life objects of any size. Parametric modeling allows modify your design by going back into your model history and changing its parameters.

Proper citation: FreeCAD (RRID:SCR_022535) 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/kalininalab/d-StructMAn

Software tool provides annotation of non-synonymous single nucleotide variants in context of structural properties of resulting amino acid changes in corresponding proteins. Improved implementation of StructMAn, shipped in container form and extended to annotation of short in-frame indels and alterations arising as consequence of alternative splicing events. Produces range of structural features by combining information from experimentally resolved structures of many related proteins, which is unique feature of StructMAn family tools. Can also harness all protein structure models stored in AlphaFold Protein Structure Database.

Proper citation: d-StructMAn (RRID:SCR_022534) Copy   

•   Source: SciCrunch Registry

http://www.nutrisurvey.de/

Software tool for nutrition calculations and surveys.

Proper citation: NutriSurvey (RRID:SCR_022655) 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://github.com/lh3/calN50/

Software tool as simple script to calculate N50/NG50 and auN/auNG.

Proper citation: calN50 (RRID:SCR_022015) Copy   

•   Source: SciCrunch Registry

https://github.com/Hi5App

Software cross platform mobile application that supports 2D/3D/4D image visualization, multi-morphometry annotation, proofreading, interactive imaging system controlling, and distributed collaboration.

Proper citation: Hi5App (RRID:SCR_022819) Copy   

•   Source: SciCrunch Registry

https://drawio-app.com/product/

Software tool as diagramming application that enables collaboration in real time.

Proper citation: draw.io (RRID:SCR_022939) Copy   

•   Source: SciCrunch Registry

https://github.com/sapporo-wes/sapporo-service

Software for standard implementation conforming to Global Alliance for Genomics and Health Workflow Execution Service API specification.

Proper citation: Sapporo service (RRID:SCR_023202) Copy   

•   Source: SciCrunch Registry

https://www.jmp.com/en_us/home.html

Statistical software tool. Predictive analytics software. Offers all tools in JMP plus advanced features for more sophisticated analyses.

Proper citation: SAS JMP Pro (RRID:SCR_022199) 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://github.com/HMPNK/CSA2.6

Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions.

Proper citation: Chromosome Scale Assembler (RRID:SCR_017960) Copy   

•   Source: SciCrunch Registry

https://github.com/jfarek/xatlas

Software tool as variant caller for SNVs and small indels. Implemented as software application written in C++ .

Proper citation: xAtlas (RRID:SCR_022987) Copy   

•   Source: SciCrunch Registry

https://www.starrlifesciences.com/product/small-animal-pulse-oximeter/

Software is part of MouseOx Plus pulse oximeter system.

Proper citation: Starr Life Sciences MouseOx Plus (RRID:SCR_022984) Copy   

•   Source: SciCrunch Registry

https://github.com/jupyter/jupyter_console

Terminal based console frontend for Jupyter kernels. This code is based on single process IPython terminal.

Proper citation: Jupyter-console (RRID:SCR_018414) Copy   

•   Source: SciCrunch Registry

http://www.nanotomy.org/OA/Sjollema2016MI/

ImageJ macro to detect, mark and count electron dense markers like goldgrains or quantum dots in electron micrographs.

Proper citation: Golddigger (RRID:SCR_020960) Copy   

•   Source: SciCrunch Registry

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

Software tool to extend unittest to make testing easier. Python unit test framework. Note, Nose has been in maintenance mode for the past several years and will likely cease without a new person/team to take over maintainership. New projects should consider using Nose2, py.test, or just plain unittest/unittest2.

Proper citation: Python Nose (RRID:SCR_018418) Copy   

•   Source: SciCrunch Registry