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http://www.agriculturalsoftwareconsultants.com/mixitwin

Professional feed formulation software for Windows 10 and Macs by Agricultural Software Consultants Inc. Complete feed formulation solution for professional nutritionists and feed producers. Software offers ingredient databases for various domesticated and wild species.

Proper citation: MixitWin (RRID:SCR_017553) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/EpiDISH/

Software R package provides tools to infer proportions of priori known cell-types present in sample representing mixture of such cell-types. Comparison of reference based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies.

Proper citation: EpiDISH R package (RRID:SCR_018004) Copy   

•   Source: SciCrunch Registry

https://colororacle.org/

Software tool as free color blindness simulator for Windows, Mac and Linux. Design for Color Impaired. Takes guesswork out of designing for color blindness by showing you in real time what people with common color vision impairments will see.Color Oracle is open source, available on GitHub for Mac and Windows/Java.

Proper citation: Color Oracle (RRID:SCR_018400) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/HomoeologPrimer

Software tool as script used to design primers for homoeologs, to amplify either homoeolog specific or all homoeologs.

Proper citation: HomoeologPrimer (RRID:SCR_017559) Copy   

•   Source: SciCrunch Registry

https://www.google.com/sheets/about/

Spreadsheet program included as part of free, web-based software office suite offered by Google within its Google Drive service. Service also includes Google Docs and Google Slides, word processor and presentation program respectively.

Proper citation: Google Sheets (RRID:SCR_017679) Copy   

•   Source: SciCrunch Registry

https://www.molinspiration.com/

Broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation, calculation of various molecular properties needed in QSAR, molecular modelling and drug design, high quality molecule depiction, molecular database tools supporting substructure and similarity searches. Molinspiration tools are platform independent and may be run on any PC, Mac, UNIX or LINUX machine. Software is distributed in form of engines, which may be used as stand-alone computational engines, used to power web-based tools, or incorporated into larger in-house Java applications.

Proper citation: Molinspiration (RRID:SCR_018525) Copy   

•   Source: SciCrunch Registry

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

Software general R package providing standard methods for meta analysis.

Proper citation: meta (RRID:SCR_019055) Copy   

•   Source: SciCrunch Registry

https://www.sqlite.org/index.html

Relational database management system contained in C library. SQLite is not client server database engine but it is embedded into the end program.

Proper citation: SQLite (RRID:SCR_017672) Copy   

•   Source: SciCrunch Registry

https://github.com/a-ludi/dentist

Software as automated pipeline method to close gaps in assemblies with long reads. Used to close assembly gaps using long reads at high accuracy.

Proper citation: DENTIST (RRID:SCR_021856) Copy   

•   Source: SciCrunch Registry

https://imbalanced-learn.org/stable/

Software Python package to tackle curse of imbalanced datasets in machine learning.Offers number of re-sampling techniques commonly used in datasets showing strong between class imbalance.

Proper citation: imblearn (RRID:SCR_021698) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/peppy/

Software python package for reading Portable Encapsulated Projects or PEPs in python.

Proper citation: peppy (RRID:SCR_021078) Copy   

•   Source: SciCrunch Registry

https://github.com/zhuangjun1981/corticalmapping

Software package for basic visual stimulation, imaging analysis, plotting, and cell visual response properties analysis functionality for calcium imaging.

Proper citation: corticalmapping (RRID:SCR_021871) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/eido/

Software validation tool for Portable Encapsulated Projects or PEPs in python.

Proper citation: eido (RRID:SCR_021076) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=CCP

Software R package for significance tests for canonical correlation analysis, including asymptotic tests and Monte Carlo method.

Proper citation: CCP (RRID:SCR_021745) Copy   

•   Source: SciCrunch Registry

https://github.com/portugueslab/stytra

Open source software Python package to control stimulation and track behaviour.Provides timed stimulus presentation, interfacing with external devices and simultaneous real time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely swimming and head restrained preparations.

Proper citation: Stytra (RRID:SCR_021500) Copy   

•   Source: SciCrunch Registry

https://github.com/openworm/tracker-commons

Software tool as repository of documentation, software, and discussions to share worm tracking data and analysis routines.Open access repository for storing, accessing, and filtering data; interchange format for notating single or multi worm behavior; and file formats written in Python for feature extraction, review, and analysis.

Proper citation: Worm Behavior Platform (RRID:SCR_021501) Copy   

•   Source: SciCrunch Registry

https://usegalaxy.eu

Software tools for analysis of data independent acqusition type proteomics data are implemented in Galaxy framework. Enables complete DIA data analysis including spectral library generation based on DDA type data, analysis of DIA data in raw or mzml format, and differntial statistical analysis. All tools are based on open-source software such as diypasef, OpenSwath, swath2stats and MSstats.

Proper citation: Data independent acquisition proteomics workbench (RRID:SCR_021862) Copy   

•   Source: SciCrunch Registry

https://github.com/zeyang-shen/maggie

Software Python package for identifying motifs mediating transcription factor binding and function. Links mutations of motif to changes of epigenomic feature without assuming linear relationship.

Proper citation: Motif Alteration Genome wide to Globally Investigate Elements (RRID:SCR_021903) Copy   

•   Source: SciCrunch Registry

https://github.com/bi-compbio/scrnax/

Software pipeline to improve gene annotation for cross species analysis of single cell RNA-Seq. Cross-species transfer of high quality 3’UTR annotation for single cell RNA-Seq.

Proper citation: scRNAx (RRID:SCR_022091) Copy   

•   Source: SciCrunch Registry

https://github.com/gatech-genemark/ProtHint

Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences.

Proper citation: ProtHint (RRID:SCR_021167) Copy   

•   Source: SciCrunch Registry