Update README.md

dbespiatykh · Aug 23, 2024 · 3ca0f13 · 3ca0f13
1 parent aec13fe
commit 3ca0f13
Showing 1 changed file with 20 additions and 1 deletion.
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 <p align="center">
-  <img src="logo.png" alt="gopiscator Logo" height=200>
+  <img src="https://github.com/dbespiatykh/gopiscator/blob/main/logo.png?raw=true" alt="gopiscator logo" height=200>
 </p>
 <hr>
 
@@ -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                                        |