diff --git a/README.md b/README.md index 7251483..4dba152 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@

- gopiscator Logo + gopiscator logo


@@ -29,6 +29,7 @@ Options: -v, --version Show the version and exit. -h, --help Show this message and exit. ``` + > [!NOTE] > `gene-list` should have your genes of interest, one gene per line: > || @@ -45,3 +46,21 @@ Options: >| Rv0002 | GO:0046677,GO:0006260 | >| Rv0003 | GO:0009432,GO:0000731,GO:0006260 | >| Rv0005 | GO:0046677,GO:0006265,GO:0006261 | + + +> [!TIP] +> If you do not provide `-o, --output` then the results will be shown in terminal like this: +>``` +>╒════╤════════════╤════════════════════╤═══════════════════════════════╤═══════════╤════════════════════╤═══════════════╕ +>│ │ GOID │ Ontology │ GO_term_name │ P-value │ Enrichment_score │ Rich_factor │ +>╞════╪════════════╪════════════════════╪═══════════════════════════════╪═══════════╪════════════════════╪═══════════════╡ +>│ 0 │ GO:0045926 │ biological_process │ negative regulation of growth │ 0 │ 4.36 │ 0.2 │ +>├────┼────────────┼────────────────────┼───────────────────────────────┼───────────┼────────────────────┼───────────────┤ +>│ 1 │ GO:0098754 │ biological_process │ detoxification │ 0.015 │ 1.82 │ 0.2 │ +>╘════╧════════════╧════════════════════╧═══════════════════════════════╧═══════════╧════════════════════╧═══════════════╛ +>``` +> When the `-o, --output` is provided the the output file will look like this: +>| GOID | Ontology | GO_term_name | Definition | P-value | FDR | Enrichment_score | Fold_enrichment | Rich_factor | GeneRatio | BgRatio | Count | Genes | +>| ---------- | ------------------ | ----------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ---------- | ---------- | ---------------- | --------------- | ----------- | --------- | --------- | ----- | ------------------------------------------------------------- | +>| GO:0045926 | biological_process | negative regulation of growth | Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. [GOC:go_curators] | 4.40E-05 | 0.00171655 | 4.35640751 | 9.81395349 | 0.1627907 | 7[35] | 43[2110] | 7 | Rv0299,Rv0609,Rv1114,Rv2010,Rv2866,Rv3384c,Rv3697c | +>| GO:0098754 | biological_process | detoxification | Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance. [GOC:dos] | 0.01503798 | 0.29324058 | 1.82281055 | 15.0714286 | 0.25 | 3[35] | 12[2110] | 3 | Rv1560,Rv2550c,Rv2801A |