update readme

person-c · Apr 19, 2024 · eaef657 · eaef657
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diff --git a/README.Rmd b/README.Rmd
@@ -22,17 +22,17 @@ knitr::opts_chunk$set(
 
 [MSigDB](https://www.gsea-msigdb.org/gsea/msigdb/) is a widely used gene set database in bio-research. However, navigating and querying pathways of interest on its website can be challenging. This R package is designed to facilitate more convenient and efficient querying of pathways either based on specific genes or using regular expression patterns to match pathway names.
 
-# Installation
+## Installation
 
 You can install the development version of r4msigdb like so:
 
 ```{r, eval=FALSE}
 devtools::install('snowGlint/r4msigdb')
 ```
 
-# Querying Pathways
+## Querying Pathways
 
-## Search for Pathways Related to a Specific Topic
+### Search for Pathways Related to a Specific Topic
 
 To retrieve pathways related to a specific topic (e.g., cell programmed death):
 
@@ -43,7 +43,7 @@ query(species = 'Hs', pathway = 'OPTOSIS') |> head()
 
 This will return a list of pathways associated with `OPTOSIS` and the genes involved in each pathway.
 
-## Search for Pathways Related to Specific Genes
+### Search for Pathways Related to Specific Genes
 
 If you want to find pathways related to specific genes (e.g., PTPRC and TP53):
 
@@ -53,7 +53,7 @@ query(species = 'Hs', symbols = c('PTPRC', 'TP53')) |> head()
 
 This will provide pathways where the specified genes are involved.
 
-## Custom Query
+### Custom Query
 
 Advanced users familiar with data.table can perform custom queries. For example, to retrieve all pathways `collection_name == 'H'`:
 
@@ -67,7 +67,7 @@ You can also use `.unlist = TRUE` to unlist the symbols column in any of the abo
 query(species = 'Hs', .unlist = TRUE) |> head()
 ```
 
-# GSEA
+## GSEA
 
 ```{r, eval=FALSE}
 library(fgsea)

diff --git a/README.md b/README.md
@@ -16,17 +16,17 @@ designed to facilitate more convenient and efficient querying of
 pathways either based on specific genes or using regular expression
 patterns to match pathway names.
 
-# Installation
+## Installation
 
 You can install the development version of r4msigdb like so:
 
 ``` r
 devtools::install('snowGlint/r4msigdb')
 ```
 
-# Querying Pathways
+## Querying Pathways
 
-## Search for Pathways Related to a Specific Topic
+### Search for Pathways Related to a Specific Topic
 
 To retrieve pathways related to a specific topic (e.g., cell programmed
 death):
@@ -56,7 +56,7 @@ query(species = 'Hs', pathway = 'OPTOSIS') |> head()
 This will return a list of pathways associated with `OPTOSIS` and the
 genes involved in each pathway.
 
-## Search for Pathways Related to Specific Genes
+### Search for Pathways Related to Specific Genes
 
 If you want to find pathways related to specific genes (e.g., PTPRC and
 TP53):
@@ -84,7 +84,7 @@ query(species = 'Hs', symbols = c('PTPRC', 'TP53')) |> head()
 
 This will provide pathways where the specified genes are involved.
 
-## Custom Query
+### Custom Query
 
 Advanced users familiar with data.table can perform custom queries. For
 example, to retrieve all pathways `collection_name == 'H'`:
@@ -126,7 +126,7 @@ query(species = 'Hs', .unlist = TRUE) |> head()
 #> 6:              C1            MT MT-ATP6
 ```
 
-# GSEA
+## GSEA
 
 ``` r
 library(fgsea)

diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd
@@ -31,17 +31,17 @@ knitr::opts_chunk$set(
 
 [MSigDB](https://www.gsea-msigdb.org/gsea/msigdb/) is a widely used gene set database in bio-research. However, navigating and querying pathways of interest on its website can be challenging. This R package is designed to facilitate more convenient and efficient querying of pathways either based on specific genes or using regular expression patterns to match pathway names.
 
-# Installation
+## Installation
 
 You can install the development version of r4msigdb like so:
 
 ```{r, eval=FALSE}
 devtools::install('snowGlint/r4msigdb')
 ```
 
-# Querying Pathways
+## Querying Pathways
 
-## Search for Pathways Related to a Specific Topic
+### Search for Pathways Related to a Specific Topic
 
 To retrieve pathways related to a specific topic (e.g., cell programmed death):
 
@@ -52,7 +52,7 @@ query(species = 'Hs', pathway = 'OPTOSIS') |> head()
 
 This will return a list of pathways associated with `OPTOSIS` and the genes involved in each pathway.
 
-## Search for Pathways Related to Specific Genes
+### Search for Pathways Related to Specific Genes
 
 If you want to find pathways related to specific genes (e.g., PTPRC and TP53):
 
@@ -62,7 +62,7 @@ query(species = 'Hs', symbols = c('PTPRC', 'TP53')) |> head()
 
 This will provide pathways where the specified genes are involved.
 
-## Custom Query
+### Custom Query
 
 Advanced users familiar with data.table can perform custom queries. For example, to retrieve all pathways `collection_name == 'H'`:
 
@@ -76,7 +76,7 @@ You can also use `.unlist = TRUE` to unlist the symbols column in any of the abo
 query(species = 'Hs', .unlist = TRUE) |> head()
 ```
 
-# GSEA
+## GSEA
 
 ```{r, eval=FALSE}
 library(fgsea)