Shore binom test
From SHORE wiki
shore binom_test can be used to evaluate two sets of count data agaist each other using a binomial test.
Command line options
Usage: shore binom_test [OPTIONS]
| Allowed options | ||
| -i, --input-file=<arg> | (Default: stdin) | Read count input file |
| -o, --output-file=<arg> | (Default: stdout) | Output file |
| -p, --distribution-p=<arg> | (Default: 0.5) | Parameter p of the binomial distribution |
| -n, --normalization-file=<arg> | File with scaling factors for each column (overrides '-p') | |
| -a, --alternative=<arg> | (Default: less) | Specifies the alternative hypothesis for the test (less or greater or twosided) |
| -1, --first-column=<arg> | Name of the first read count column | |
| -2, --2nd-column=<arg> | Name of the second read count column (tested vs. column 1) | |
| --global-scaling=<arg> | (Default: 1) | Scaling constant with wich all read counts are multiplied |
| -j, --input-header=<arg[,...]> | Specify header for input file, if not available | |
| -f, --fold-change | Report fold enrichment values | |
| --fdr-bh | Calculate Benjamini-Hochberg FDR | |
| --sort | Sort output | |
