A useful introduction to the survival package:
http://www.sthda.com/english/wiki/cox-proportional-hazards-model (http://www.sthda.com/english/wiki/survival-analysis-basics)
An Ensembl based database that contains cross references, and annotation information on multiple organisms. Vignette on Ensembl annotation
A great summary on how to make your Markdown documents more user friendly and easier to follow by the Posit team:
<details>
<summary>Exciting code</summary>
</details>
Show header
title: "HLA II promiscuity"
author: "Gergely Koppány"
date: "`r Sys.Date()`"
output:
html_notebook:
code_folding: hide
collapsed: yes
fig_caption: yes
fig_height: 4
fig_width: 5
smooth_scroll: yes
theme: sandstone
toc: yes
toc_depth: 5
toc_float: yes
number_sections: true
Nextflow offers multiple well documented and reproducible data analysis pipelines which should be considered, if reproducibility and convenience is important. Nextflow's RNAseq pipeline
Salmon analyses RNAseq data, and can determine, the strandedness, and other experimental parameters of the data, it it is unknown.
Salmon to determine strandedness, [https://salmon.readthedocs.io/en/latest/index.html](Salmon documentation)
RSEM is a transcript quantification tool, that can determine the transcript isoform, and gene counts from a BAM filke aligned to the transcriptome. RSEM Documentation
Another RNAseq quantification tool, that can quantify gene counts from a genome aligned BAM file. Is part of the Subread software package. Documentation