Spelling corrections

Author: nvelden

DESCRIPTION

@@ -13,6 +13,7 @@ Description: 'geneviewer' is an R package for plotting gene clusters and
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
+Language: en-US
 RoxygenNote: 7.3.1
 URL: https://github.com/nvelden/geneviewer
 BugReports: https://github.com/nvelden/geneviewer/issues

NEWS.md

@@ -12,7 +12,7 @@
 # geneviewer 0.1.6
 
 ### Enhancements:
-- Option to perfrom BlastP between gene clusters.
+- Option to perform BlastP between gene clusters.
 - Add option to add links between genes in clusters.
 
 # geneviewer 0.1.5

R/read_genbank.R

@@ -1,6 +1,6 @@
 #' Read Data from GenBank Files
 #'
-#' This function reads data from a single GenBank file or directorty with
+#' This function reads data from a single GenBank file or directory with
 #' GenBank files. It allows selective extraction of information by specifying
 #' sections and features.
 #'

man/read_gbk.Rd

@@ -80,7 +80,7 @@ BlastP_results <- geneviewer::protein_blast(
 )
 ```
 
-After running the BlastP, the dataset will contain three additional columns. These colums are:
+After running the BlastP, the dataset will contain three additional columns. These columns are:
 
 -   **BlastP**: Indicates the top BlastP match found within the query cluster, characterized by its unique protein id.
 -   **identity**: The percentage identity to the BlastP hit.
@@ -91,7 +91,7 @@ After running the BlastP, the dataset will contain three additional columns. The
 kable(head(BlastP_results %>% select(-translation)))
 ```
 
-We can visualize the results using `geneviewer`. In the graph the clusters are ordered based on the synteny score. The genes are colored by the BlasP hit found in the query cluster. Genes that remain uncolored did not have any significant homologous. By hoovering over the genes one can see the percentage identity and similarity.
+We can visualize the results using `geneviewer`. In the graph the clusters are ordered based on the synteny score. The genes are colored by the BlastP hit found in the query cluster. Genes that remain uncolored did not have any significant homologous. By hoovering over the genes one can see the percentage identity and similarity.
 
 ```{r echo = TRUE, results='asis'}
 GC_chart(

vignettes/BLASTP.Rmd

@@ -135,7 +135,7 @@ chart %>%
 
 ### Loading Multiple GenBank files
 
-The above functions to read and transfom .gbk files can also be used to load multiple .gbk files from a folder and shown the clusters side by side. To demonstrate this we can go to the cluster page for [BGC0000001](https://mibig.secondarymetabolites.org/repository/BGC0000001/index.html#r1c1) and navigate to the "KnownClusterBlast" page. Click on the homologous clusters and download the .gbk files for [BGC0001694](https://mibig.secondarymetabolites.org/repository/BGC0001694/index.html#r1c1), [BGC0001492](https://mibig.secondarymetabolites.org/repository/BGC0001492/index.html#r1c1), [BGC0001288](https://mibig.secondarymetabolites.org/repository/BGC0001288/index.html#r1c1) and [BGC0000133](https://mibig.secondarymetabolites.org/repository/BGC0000133/index.html#r1c1).  
+The above functions to read and transform .gbk files can also be used to load multiple .gbk files from a folder and shown the clusters side by side. To demonstrate this we can go to the cluster page for [BGC0000001](https://mibig.secondarymetabolites.org/repository/BGC0000001/index.html#r1c1) and navigate to the "KnownClusterBlast" page. Click on the homologous clusters and download the .gbk files for [BGC0001694](https://mibig.secondarymetabolites.org/repository/BGC0001694/index.html#r1c1), [BGC0001492](https://mibig.secondarymetabolites.org/repository/BGC0001492/index.html#r1c1), [BGC0001288](https://mibig.secondarymetabolites.org/repository/BGC0001288/index.html#r1c1) and [BGC0000133](https://mibig.secondarymetabolites.org/repository/BGC0000133/index.html#r1c1).  
 
 We place all the.gbk files in the same directory and can load them all together as we have done previously.
 

vignettes/LoadGenBankFiles.Rmd

@@ -19,7 +19,7 @@ knitr::opts_chunk$set(
 
 ### Intro
 
-This tutorial guides you through the process of performing genome alignments using [MUMmer](https://mummer4.github.io/index.html), an alignment tool widely used for comparing genomic sequences. As an example we will align the plasmids from serveral species of *B. thuringiensis*. Following the alignment, we'll show you how to visualize the results using **`geneviewer`**.
+This tutorial guides you through the process of performing genome alignments using [MUMmer](https://mummer4.github.io/index.html), an alignment tool widely used for comparing genomic sequences. As an example we will align the plasmids from several species of *B. thuringiensis*. Following the alignment, we'll show you how to visualize the results using **`geneviewer`**.
 
 ### Materials