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http://trimal.cgenomics.org/

Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses.

Proper citation: trimAl (RRID:SCR_017334) Copy   

•   Source: SciCrunch Registry

https://arxiv.org/abs/1308.2012

Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics.

Proper citation: GCE (RRID:SCR_017332) Copy   

•   Source: SciCrunch Registry

https://www.cmrr.umn.edu/downloads/mrspa

Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab.

Proper citation: MRspa (RRID:SCR_017292) Copy   

•   Source: SciCrunch Registry

https://github.com/NHLBI-BCB/IKAP

Software tool for identifying K mAjor cell population groups in single-cell RNA-seq analysis. Algorithm identifying major cell groups that improves differentiating by tuning parameters for clustering. Using multiple datasets improves identification of major cell types and facilitates cell ontology curation.

Proper citation: IKAP (RRID:SCR_017417) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Glimma.html

Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data.

Proper citation: Glimma (RRID:SCR_017389) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/tdtdecodingtoolbox/

Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data.

Proper citation: The Decoding Toolbox (RRID:SCR_017424) Copy   

•   Source: SciCrunch Registry

https://www.beast2.org/

Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager.

Proper citation: BEAST2 (RRID:SCR_017307) Copy   

•   Source: SciCrunch Registry

https://github.com/ISUgenomics/SequelQC

Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data.

Proper citation: SequelQC (RRID:SCR_017279) Copy   

•   Source: SciCrunch Registry

https://www.qtiplot.com/

Software tool for data analysis and scientific visualization by IONDEV SRL.

Proper citation: QtiPlot (RRID:SCR_017311) Copy   

•   Source: SciCrunch Registry

http://www.bioisis.net

Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets.

Proper citation: SCÅTTER (RRID:SCR_017271) Copy   

•   Source: SciCrunch Registry

https://depmap.org/portal/

Portal for identifying genetic and pharmacologic dependencies and biomarkers that predicts them by providing access to datasets, visualizations, and analysis tools that are being used by Cancer Dependency Map Project at Broad Institute. Project to systematically identify genes and small molecule dependencies and to determine markers that predict sensitivity. All data generated by DepMap Project are available to public under CC BY 4.0 license on quarterly basis and pre-publication.

Proper citation: Cancer Dependency Map Portal (RRID:SCR_017655) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-assays-analysis/western-blotting/detect-proteins-western-blot/western-blot-imaging-analysis/ibright-western-blot-imaging-systems/ibright-analysis-software-connectivity.html

Software for organizing and analyzing blot and gel images captured on iBright Imaging Systems. Available as desktop version PC and Mac OS compatible and cloud-based version accessible via web browser through Connect platform.

Proper citation: iBright Analysis Software (RRID:SCR_017632) Copy   

•   Source: SciCrunch Registry

https://www.mesquiteproject.org/

Software tool as modular system for evolutionary analysis. Software for evolutionary biology, designed to organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Analyses available depend on modules installed. Comes with many packages already installed.

Proper citation: Mesquite (RRID:SCR_017994) Copy   

•   Source: SciCrunch Registry

https://www.volumegraphics.com/de/produkte/vgstudio.html

Software tool for analysis and processing of µCT data, e.g. compiling virtual 3D models of morphological structures in site by Volume Graphics GmbH. Used for visualization of CT data.

Proper citation: VG Studio MAX (RRID:SCR_017997) Copy   

•   Source: SciCrunch Registry

http://mordred.bioc.cam.ac.uk/~rapper/rampage.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2021.Web based structural analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB. Used to visualize dihedral angles ψ against φ of amino acid residues in protein structure.

Proper citation: RAMPAGE (RRID:SCR_017590) Copy   

•   Source: SciCrunch Registry

http://www.jwatcher.ucla.edu

Software Java tool for quantitative analysis of behavior. Used to address any theoretical problem that requires complex sequence of actions to be scored by human observer. Runs on microcomputer providing Java Virtual Machine[TM] and has been tested on Windows[TM] and Macintosh[TM] systems. Legacy version (version 0.9) works on older systems (Macintosh OS-9 and Windows-98), while Version 1.0 works well on Macintosh OS-X and Windows XP systems. JWatcher Video works best on Windows XP systems and has reduced functionality running in Macintosh OS-X. JWatcher-Palm can be used to acquire data on Palm OS[TM] equipped device and analyze it on your main computer.

Proper citation: JWatcher (RRID:SCR_017595) Copy   

•   Source: SciCrunch Registry

https://github.com/XSLiuLab/tumor-immunogenicity-score

Repository to share analysis procedure, data and help readers or reviewers to know more detail of this work, reproduce or make use of results they are interested in.

Proper citation: TIGS (RRID:SCR_017565) Copy   

•   Source: SciCrunch Registry

https://www.libreoffice.org/

Open source software application with data analysis tools and spreadsheet templates used to manage, process and visualize data. LibreOffice Calc is spreadsheet component of LibreOffice software package developed by Document Foundation.

Proper citation: LibreOfficeCalc (RRID:SCR_018013) Copy   

•   Source: SciCrunch Registry

http://chemrich.fiehnlab.ucdavis.edu/

Software tool for chemical similarity enrichment analysis of metabolomics datasets. Used in studies to uncover biological mechanisms in organisms under genetic or environmental stress in system biology manner or finding risk factors for chronic diseases in exposome wise association studies using blood specimens. Allows users to realize pathway analysis.

Proper citation: ChemRICH (RRID:SCR_017609) Copy   

•   Source: SciCrunch Registry

https://github.com/shanemomara/omaraneurolab/tree/master/NeuroChaT

Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories.

Proper citation: NeuroChaT (RRID:SCR_018020) Copy   

•   Source: SciCrunch Registry