Tools   Select Another Resource Report Type

http://tcoffee.crg.cat/apps/tcoffee/do:regular

A multiple sequence alignment server which can align Protein, DNA and RNA sequences.

Proper citation: T-Coffee (RRID:SCR_011818) Copy   

•   Source: SciCrunch Registry

http://probcons.stanford.edu/

Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

Proper citation: ProbCons (RRID:SCR_011813) Copy   

•   Source: SciCrunch Registry

http://genevenn.sourceforge.net/

A web application creating Venn diagrams from two or three gene lists.

Proper citation: GeneVenn (RRID:SCR_012117) Copy   

•   Source: SciCrunch Registry

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Tool to search translated nucleotide databases using a protein query.

Proper citation: TBLASTN (RRID:SCR_011822) Copy   

•   Source: SciCrunch Registry

http://nhjy.hzau.edu.cn/kech/swxxx/jakj/dianzi/Bioinf6/GeneFinding/GeneFinding2.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains).

Proper citation: FGENESH (RRID:SCR_011928) Copy   

•   Source: SciCrunch Registry

http://gpcr.biocomp.unibo.it/bacello/

A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.

Proper citation: BaCelLo (RRID:SCR_011965) Copy   

•   Source: SciCrunch Registry

https://www.indicalab.com/halo/

Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology.

Proper citation: HALO (RRID:SCR_018350) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/ekmolloy/fastmulrfs

Software pipeline for estimating species trees from multi copy gene trees.

Proper citation: FastMulRFS (RRID:SCR_024505) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.project-redcap.org/

Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions.

Proper citation: REDCap (RRID:SCR_003445) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://past.en.lo4d.com/windows

Software package for education and data analysis. Used for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy.

Proper citation: PAST (RRID:SCR_019129) Copy   

•   Source: SciCrunch Registry

http://msquant.sourceforge.net/

Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine.

Proper citation: MSQuant (RRID:SCR_019206) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/biomaRt/

Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis.

Proper citation: biomaRt (RRID:SCR_019214) Copy   

•   Source: SciCrunch Registry