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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://www.schrodinger.com/protein-preparation-wizard
Software tool for correcting common structural problems and creating reliable, all atom protein models.
Proper citation: Protein preparation Wizard (RRID:SCR_016749) Copy
https://www.openepi.com/Menu/OE_Menu.htm
Web based, open source, operating system independent series of programs designed for use in public health and medicine for training or practice that provide number of epidemiologic and statistical tools for summary data. Developed in JavaScript and HTML, and can be run in modern web browsers. Program can be run from OpenEpi website or downloaded and run without web connection.
Proper citation: OpenEpi (RRID:SCR_021913) Copy
https://github.com/Tarskin/LaCyTools
Software high throughput data extraction package for LC-MS data.Targeted Liquid Chromatography-Mass Spectrometry data processing package for relative quantitation of glycopeptides.
Proper citation: LaCyTools (RRID:SCR_024525) Copy
https://CRAN.R-project.org/package=GOplot
Software R package for visually combining expression data with functional analysis.
Proper citation: GOplot (RRID:SCR_024419) Copy
https://CRAN.R-project.org/package=geepack
Software R package implements generalized estimating equations for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can handle clustered categorical responses. Used for fitting marginal generalized linear models to clustered data.
Proper citation: geepack (RRID:SCR_024510) Copy
https://cran.r-project.org/web/packages/dagitty/
Software R package provides access to all of the capabilities of DAGitty web application for drawing and analysing Directed Acyclic Graphs within the R platform for statistical computing. Used for graphical analysis of structural causal models.
Proper citation: DAGitty (RRID:SCR_024509) Copy
https://github.com/ekmolloy/fastmulrfs
Software pipeline for estimating species trees from multi copy gene trees.
Proper citation: FastMulRFS (RRID:SCR_024505) Copy
http://www.cs.cmu.edu/~durand/Notung/
Software package to facilitate large scale analysis, using both rooted and unrooted trees.Used for dating gene duplications and optimizing gene family trees.Used for inferring duplication dates from gene trees automatically and can also be used as exploratory analysis tool for evaluating alternative hypotheses.
Proper citation: NOTUNG (RRID:SCR_024484) Copy
https://CRAN.R-project.org/package=CMplot
Software drawing R package designed for Manhattan plot of genomic analysis.
Proper citation: CMplot (RRID:SCR_024514) Copy
https://github.com/PoisonAlien/Maftools
Software R package offers multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses. Maftools requires somatic variants in Mutation Annotation Format (MAF) and is independent of larger alignment files.
Proper citation: maftools (RRID:SCR_024519) Copy
https://gitlab.inria.fr/Phylophile/Treerecs
Open source, species and gene tree reconciliation software. Software integrated phylogenetic tool, from sequences to reconciliations. Used to correct, rearrange and reroot gene trees with regard to given species tree.
Proper citation: Treerecs (RRID:SCR_024497) Copy
Ratings or validation data are available for this resource
http://broadinstitute.github.io/picard/
Java toolset for working with next generation sequencing data in the BAM format.
Proper citation: Picard (RRID:SCR_006525) Copy
Software package for statistical analysis and presentation of graphics. Statistical software for data science.
Proper citation: Stata (RRID:SCR_012763) Copy
https://github.com/ElsevierSoftwareX/SOFTX-D-15-00082
Software PCA-based toolkit for compression and analysis of molecular simulation data. Used for compression and analysis of molecular dynamics (MD) simulation data.
Proper citation: pyPCcazip (RRID:SCR_024423) Copy
http://www-stat.stanford.edu/~tibs/SAM/
Software for genomic expression data mining using a statistical technique for finding significant genes in a set of microarray experiments.
Proper citation: SAM (RRID:SCR_010951) Copy
https://www.statease.com/software/design-expert/
Statistical software package from Stat-Ease Inc. to perform design of experiments. Offers comparative tests, screening, characterization, optimization, robust parameter design, mixture designs and combined designs.
Proper citation: Design-Expert (RRID:SCR_022671) Copy
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