run-dea

Run differential expression (DE)

usage: run-dea [--help] [--batch]
               [--lfcThreshold LFCTHRESHOLD] [--alpha ALPHA]
               [--symbolCol SYMBOLCOL] [--orfCol ORFCOL] [--delim DELIM]
               [--lfcShrinkMethod LFCSHRINKMETHOD] config

Positional arguments

config

Yaml config file (same as used for run-htseq-workflow)

Flags

-h, --help

show this help message and exit

-b, --batch

Use ‘batch’ from sample table

Optional Arguments

-l, --lfcThreshold

LFC threshold [default: log2(1.2)]

-a, --alpha

FDR threshold [default: 0.05]

-s, --symbolCol

Column for features (symbol/names) - HTSeq workflow only [default: 2]

-o, --orfCol

Column for ORF types - HTSeq workflow only

-d, --delim

Field separator for the count tables {TAB,CSV} [default: TAB]

--lfcShrinkMethod

LFC shrinkage method {apeglm,ashr} [default: apeglm]