In this post, we will compare STAR --quantMode GeneCounts vs HTSeq. Their goal is to perform gene quantification during or after read mapping, respectively. To achieve this, they need a…
In this post, we will see where to download some reference files that are required for the analysis of RNA sequencing and SNP genotyping data. Genome versions The current genome…
This post compiles 7 useful Linux commands in bioinformatics with examples: cat, wc, du, grep, awk, sed, and find. However, I will not review pwd, mkdir, cd, ls, mv, rm,…
There are several ways to use a Linux terminal on Windows, each one having its own pros and cons. Dual booting A dual booting is the installation of two operating…
In this blog post, we will see how to connect to an HPC (High Performance Computer) on Windows. During my studies, I used the Putty software to do that but…
In this blog post, we will see how to import VCF files in base R. This type of file is very common in genotyping analyses but requires a specific method…
Do you want to learn how to import FASTA files in base R? This particular type of bioinformatics file is difficult but not impossible to import using base R functions.…
To sort colors by hue in R, we need to convert the colors from HEX (hexadecimal) to RGB (red-green-blue), compute the hue values and then sort them. Example The I…
To convert colors from the RGB (red-green-blue) to the HCL (hue-chroma-lightness) system in R (or any other software), we need to go through XYZ and CIE-LAB color systems. What is…
In this tutorial, we will see how to convert colors from the RGB (red-green-blue) to the HSL (hue-saturation-lightness), HSV (hue-saturation-value) or HSI (hue-saturation-intensity) systems in R (and vice versa). If…
In this post, we will see how to convert colors from the RGB (red-green-blue) to the HEX (hexadecimal) system in R (and vice versa). For that, we will use base…
In this post, we will see how to use different R color palettes in base R plots such as the barplot function. Color palettes from base R First, we can…
This week, we will see how to connect two points with a straight line in base R and ggplot2. For this, we need to compute the slope and the intercept.…
We will see how to perform exponential regressions and how to plot these curved regression lines in base R and ggplot2, using the lines and geom_line functions, respectively. Please read…
In this tutorial, we will see how to perform a local polynomial regression using the loess function and how to plot curved regression lines in base R and ggplot2. We…
We will see how to perform a linear regression using the lm function and to plot these straigth regression lines in base R and ggplot2, using the lines and geom_abline…
In this article, we will see how to add straight (vertical, horizontal and diagonal) lines to plots in base R and in ggplot2. As an example, we will use the…
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