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https://github.com/lrq3000/spm_auto_reorient_coregister

Open source cross platform for automatic AC-PC realignment, reorientation and coregistration robust to brain damage in Statistical Parametric Mapping. Set of routines to perform auto reorient and auto coregistration in toolbox SPM12.

Proper citation: spm_auto_reorient_coregister (RRID:SCR_017281) Copy   

•   Source: SciCrunch Registry

https://github.com/QTIM-Lab/DeepNeuro

Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners.

Proper citation: DeepNeuro (RRID:SCR_016911) Copy   

•   Source: SciCrunch Registry

https://github.com/missy139/PreSurgMapp

A MATLAB toolbox for processing the functional areas of the brain using multi-modal fMRI data for pre-surgical mapping. It is composed of three types of individual-level ICA analyses for user use. Traditional ICA (task) can be used for task fMRI. Either Traditional ICA (rest) or ICA with DICI (rest) can be used for rs-fMRI. Traditional ICA (rest) is designed for users who already have a hypothesis of the pattern of the target component and want to have manually set components by themselves. ICA with DICI (rest) is completely automatic, given that the user provides a template (provided). The software utilizes an automatic component identification method that is based on the discriminatory-index. All the components from multiple ICA runs with multiple component settings are ranked and compiled.

Proper citation: PreSurgMapp (RRID:SCR_014427) Copy   

•   Source: SciCrunch Registry

https://github.com/bio2bel

Software Python package enabling Biological Expression Language to act as semantic integration layer for multi modal and multi scale data sets in life sciences. Used for integrating biological databases and structured data sources in BEL. Has ability to support curation of pathway mappings, integration of pathway databases, and machine learning applications.

Proper citation: Bio2BEL (RRID:SCR_017659) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html

Software package which brings to R color scales. Created for the Python matplotlib library.

Proper citation: viridis (RRID:SCR_016696) Copy   

•   Source: SciCrunch Registry

http://prospector.ucsf.edu

A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass.

Proper citation: Protein Prospector (RRID:SCR_014558) Copy   

•   Source: SciCrunch Registry

http://www.acdlabs.com/resources/freeware/nmr_proc/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 27, 2016. A software package that provides 1D and 2D NMR tools as well as processing and interpretation for all other major analytical techniques (LC/MS, IR, Raman, and more) in one package. It also has support for structure verification and multiplet reports.

Proper citation: ACD/ NMR Processor (RRID:SCR_014679) 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://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/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.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://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

https://sourceforge.net/projects/r8s/

Software package for estimating absolute rates of molecular evolution and divergence times on phylogenetic tree. Divergence time estimation on phylogenies.

Proper citation: r8s (RRID:SCR_021161) Copy   

•   Source: SciCrunch Registry

https://artistoo.net

Software toolbox, formerly called CPMjs, as framework to build interactive, explorable simulation models of cells and tissues in web browser. JavaScript library to build interactive Cellular Potts Models as command line applications or in web browser.

Proper citation: Artistoo (RRID:SCR_020983) 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://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://cran.r-project.org/web/packages/gtsummary/index.html

Software R package creating customizable presentation ready tables, summarizing data sets, regression models, and more. Used for publication ready data summary and analytic result tables.

Proper citation: gtsummary (RRID:SCR_021319) 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://estech.shinyapps.io/prisma_flowdiagram/

Software R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams. ShinyApp for producing PRISMA 2020 compliant flow diagrams.

Proper citation: PRISMA2020 (RRID:SCR_021053) Copy   

•   Source: SciCrunch Registry