NACHO - NanoString Quality Control Dashboard
NanoString nCounter data are gene expression assays where there is no need for the use of enzymes or amplification protocols and work with fluorescent barcodes (Geiss et al. (2018) <doi:10.1038/nbt1385>). Each barcode is assigned a messenger-RNA/micro-RNA (mRNA/miRNA) which after bonding with its target can be counted. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA. 'NACHO' (NAnoString quality Control dasHbOard) is able to analyse the exported NanoString nCounter data and facilitates the user in performing a quality control. 'NACHO' does this by visualising quality control metrics, expression of control genes, principal components and sample specific size factors in an interactive web application.
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mirnamrnananostringnormalisationquality-controlshiny
5.53 score 9 stars 38 scripts 231 downloadsinsane - INsulin Secretion ANalysEr
A user-friendly interface, using Shiny, to analyse glucose-stimulated insulin secretion (GSIS) assays in pancreatic beta cells or islets. The package allows the user to import several sets of experiments from different spreadsheets and to perform subsequent steps: summarise in a tidy format, visualise data quality and compare experimental conditions without omitting to account for technical confounders such as the date of the experiment or the technician. Together, insane is a comprehensive method that optimises pre-processing and analyses of GSIS experiments in a friendly-user interface. The Shiny App was initially designed for EndoC-betaH1 cell line following method described in Ndiaye et al., 2017 (<doi:10.1016/j.molmet.2017.03.011>).
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beta-cellsendoc-betah1insulin-secretionpancreasshinystatisticsstats
5.48 score 3 stars 4 scripts 169 downloadsMiSTr - Mixed effects Score Test for continuous outcomes
Test for association between a set of SNPS/genes and continuous or binary outcomes by including variant characteristic information and using (weighted) score statistics.
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rare-variant-analysisstatistics
3.64 score 88 scripts