Please choose application from the list
* Strep.N.A - contains data from NGS experiments from Streptomyces coelicolor and Streptomyces venezuelae, prepared during a master thesis by Marek Skrzyński
Master thesis - Marek Skrzyński
* bioscreen reads, filters and analyzes growth curves from Bioscreen. Requires two files: plate map saved in xlsx format (example map and template available below) and bioscreen data saved in csv or in xlsx format. Data does not have to be preprocessed in any way. Outlier growth curves can be filtered out based on their absorbance values. Filtered data and plots in png or svg format can be downloaded.
* EDA - Exploratory Data Analysis - facilitates exploration of tabular datasets using plots (histrograms, boxplots, scatterplot etc) and basic statistical tests such as t-students test, anova etc. Plots can be saved in png format. Accepts data in txt ot xlsx format (multiple files can be uploaded if they have the same column order), preferably in a long tidy format (one row = one observation), but conversion from wide data format is possible. User can choose variable column for the analysis and a second group column for the comparison and filtering.
* findpeaks - allows localization of local maxima in fluorescence profiles from microscopic time-lapse movies. Localization process uses R package Peaks. Accepts data only in txt format where the first column is the length of cell and second fluorescence intensity. Data can be generated from ImageJ using script available on the Github page). Result files be downloaded in txt format. Analysis and comparison of complexes localization and fluorescence intensity of different strains can be done within the app.
* smoother Adds a trend line to fluorescence profiles of one or two fluorophores. Cells can be divided into subgroups based on the kmeans algorithm. Accepts data only in txt format where the first column is the length of cell and second fluorescence intensity. Data can be generated from ImageJ using custom script available on the Github page).
* sporecounter - calculates prespore length and segregation defects in Streptomyces sporulating hyphae. Finds septa and chromosome positions in hyphae using R package Peaks. Requires two files in txt format (DNA and cell wall fluorescence profiles) where the first column is the length of cell and second fluorescence intensity. Data can be generated from ImageJ using a custom script available on the Github page).
Example dataset for sporecounter, DNA channel
Example dataset for sporecounter, cell wall channel
Applications can be used online without R instalation (ImageJ is required for the microscope related applications)
All applications can be downloaded and installed as R packages from github. Unfortunately Peaks package required for findpeaks and sporecounter package is no longer available on CRAN, but its 0.2 version can still be installed from source or using devtools package.
All questions and problems should be addressed to Agnieszka Strzałka