---
title: "04-Run-LncFinder"
author: "Zach Bengtsson"
date: "2023-04-19"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

Load the LncFinder and associated packages for workflow...
```{r}
install.packages(c("readr", "tidyverse", "LncFinder", "GenomicRanges", "Biostrings", "rtracklayer"))

```
```{r}
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("GenomicFeatures")
```

```{r}
library(GenomicFeatures)
library(GenomicRanges)
library(Biostrings)
library(rtracklayer)
library(LncFinder)
library(tidyverse)

```
```{r}
# Use BiocManager to install the BiocGenerics package
BiocManager::install("BiocGenerics")

```
```{r}
library(BiocGenerics)
library(GenomicFeatures)
lncRNAs <- import("../output/final_lncRNAs.gtf")
genome <- import("../output/Pver_genome_assembly_v1.0-valid.gtf")
```