Below you will find pages that utilize the taxonomy term “csv”
Blog
Convert XLS/XLSX to CSV in Bash
In most of the modern Linux distributions, Libre Office is available and it can be used to convert XLS or XLSX file(s) to CSV file(s) in bash.
For XLS file(s):
1for i in *.xls; do libreoffice --headless --convert-to csv "$i"; done For XLSX file(s):
1for i in *.xlsx; do libreoffice --headless --convert-to csv "$i"; done You may get following warning but it still works fine:
1javaldx: Could not find a Java Runtime Environment!
Blog
Data Preprocessing I for Salmon Project
Since we’ll be using R for most of the analyses, we converted XLS data file to CSV using MS Office Excel 2013 and then we had to fix several lines using Sublime Text 2 because three colums in these lines were left unquoted which later created a problem reading in RStudio.
The data contains phosphorylation data of 8553 peptides. There are many missing data points for many peptides and since IPI IDs were used for peptides and these are not supported now, we had to convert IPI IDs to HGNC approved symbols although data had these symbols as names but they looked outdated.
Blog
Playing around with CellNOptR Tool and MIDAS File
With CellNOptR, we will try to construct network models for the challenge. For this, the tool needs two inputs. First one is a special data object called CNOlist that stores vectors and matrices of data. Second one is a .SIF file that contains prior knowledge network which can be obtained from pathway database and analysis tools.
CNOlist contains following fields: namesSignals, namesCues, namesStimuli and namesInhibitors, which are vectors storing the names of measurements.