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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

https://www.google.com/intl/de/forms/about/

Software for creating surveys and questionnaires.

Proper citation: Google Forms (RRID:SCR_023174) Copy   

•   Source: SciCrunch Registry

https://github.com/BGI-shenzhen/VCF2Dis

Software to calculate p-distance matrix based Variant Call Format.

Proper citation: VCF2Dis (RRID:SCR_022513) Copy   

•   Source: SciCrunch Registry

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

Software CLI tool to verify workflow reproducibility.

Proper citation: Tonkaz (RRID:SCR_023206) Copy   

•   Source: SciCrunch Registry

https://github.com/sapporo-wes/yevis-cli

Software CLI tool to support building and maintaining Yevis workflow registry.

Proper citation: Yevis cli (RRID:SCR_023204) Copy   

•   Source: SciCrunch Registry

https://www.flidea.tech/flic-support

Software tool as user interface for running Fly Liquid Food Interaction Counter experiments.

Proper citation: FLIC Monitor (RRID:SCR_018387) Copy   

•   Source: SciCrunch Registry

https://github.com/anuprulez/ml-jupyter-notebook

Open source, docker based, and GPU enabled jupyterlab notebook infrastructure that runs on public compute infrastructure of Galaxy Europe for rapid prototyping and developing end-to-end AI projects. Jupyterlab notebook in GPU enabled docker container for machine learning and deep learning.

Proper citation: Docker based GPU enabled Jupyterlab (RRID:SCR_022695) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/pyani/

Software package and script for calculation of genome scale average nucleotide identity. Python3 module that provides support for calculating average nucleotide identity and related measures for whole genome comparisons, and rendering relevant graphical summary output. Where available, it takes advantage of multicore systems, and can integrate with SGE/OGE-type job schedulers for the sequence comparisons.

Proper citation: Pyani (RRID:SCR_021088) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/org.Rn.eg.db/

Software R tool for genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers.

Proper citation: org.Rn.eg.db (RRID:SCR_018358) Copy   

•   Source: SciCrunch Registry

https://github.com/Frederik-D-Weber/zmax_edf_merge_converter

Software tool for comprehensive conversion of folder with Hypnodyne zmax EDF files into merged European Data Format.

Proper citation: zmax_edf_merge_converter (RRID:SCR_022567) Copy   

•   Source: SciCrunch Registry

https://github.com/cobilab/geco3/

Software tool as DNA compressor that uses neural network to do mixing of experts.

Proper citation: GeCo3 (RRID:SCR_018877) Copy   

•   Source: SciCrunch Registry

https://github.com/bondarevts/flucalc

Software tool as MSS-MLE calculator for Luria–Delbrück fluctuation analysis.

Proper citation: FluCalc (RRID:SCR_019322) Copy   

•   Source: SciCrunch Registry

https://www.openscad.org/

Software tool for creating solid 3D CAD objects. Used for creating 3D models focusing on CAD aspects of 3D modeling of machine parts. Reads in script file that describes object and renders 3D model from this script file.

Proper citation: OpenSCAD (RRID:SCR_018870) Copy   

•   Source: SciCrunch Registry

https://www.1ka.si/d/en

Open source software application that enables services for online surveys. Provides advanced support for all steps of web survey process. Conduct research and analysis from beginning to end.

Proper citation: 1KA (RRID:SCR_019283) Copy   

•   Source: SciCrunch Registry

https://github.com/liqiwei2000/BayesEpiModels

Software tool for accessing performance of different epidemiological models, including both growth and compartmental models, in Bayesian framework.

Proper citation: BayesEpiModels (RRID:SCR_019291) Copy   

•   Source: SciCrunch Registry