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Table 4 A-Lister Command Line Interface (CLI)

From: A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

CommandArgumentBrief Description
name-list<input-file>Full path to the input file.
<query>The query to be performed over input name lists.
-idDelimiter used in input file.
-oOutput directory.
-odDelimiter used in output file.
-vVerbose flag.
-e, −-examplesShow examples and exit.
-h, −-helpShow help/manual and exit.
diff-expression<input-file>Full path to the input file.
-dq, <direct-query>The directional query to be performed over pairwise comparisons.
-pc, <pc-mapping>Specifies the layout of pairwise comparison within the file.
-nSpecifies the ID column in file.
-fcSpecifies the fold change column(s) in file.
-s1Specifies sample1 column in file.
-s2Specifies sample2 column in file.
-fFilter parameter used to filter the files by columns/attributes.
-idDelimiter used in input file.
-oOutput directory.
-odDelimiter used in output file.
-vVerbose flag.
-e, −-examplesShow examples and exit.
-h, −-helpShow help/manual and exit.
  1. Bolded parameters are mandatory