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https://www.schrodinger.com/Prime/
Software package that uses homology modeling and fold recognition to make protein structure predictions.
Proper citation: Prime (RRID:SCR_014887) Copy
https://cran.r-project.org/web/packages/glmnet/index.html
Procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. The algorithm uses cyclical coordinate descent in a path-wise fashion.
Proper citation: glmnet (RRID:SCR_015505) Copy
http://www.atgc-montpellier.fr/phyml/
Web phylogeny server based on the maximum-likelihood principle.
Proper citation: PhyML (RRID:SCR_014629) Copy
http://rloop.bii.a-star.edu.sg/?pg=qmrlfs-finder
A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis.
Proper citation: QmRLFS-finder (RRID:SCR_014584) Copy
http://bioconductor.org/packages/release/bioc/html/topGO.html
Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
Proper citation: topGO (RRID:SCR_014798) Copy
Commercial organization that provides services and products in global healthcare and diagnostics.
Proper citation: Hologic (RRID:SCR_015529) 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
http://srv00.recas.ba.infn.it/ASPicDB/
A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation.
Proper citation: ASPicDB (RRID:SCR_002102) 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
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