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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.
Commercial organization that provides services and products in global healthcare and diagnostics.
Proper citation: Hologic (RRID:SCR_015529) Copy
http://www.biogazelle.com/qbaseplus
Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology.
Proper citation: qBasePLUS (RRID:SCR_003370) 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://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
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
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
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
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
http://genevenn.sourceforge.net/
A web application creating Venn diagrams from two or three gene lists.
Proper citation: GeneVenn (RRID:SCR_012117) Copy
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