Publications by Ghalia Malki
Portfolio 1 Assignment- Ghalia Malki
A complete bioinformatics workflow in R By: Nathan L. Brouwer “Worked example: Building a phylogeny in R” Introduction phylogenies can be used to build phylogenetic trees which can be used to show the evolutionary pathways and connections between organisms Vocab Make a list of at least 10 vocab terms that are important ascension number fas...
5035 sym R (13315 sym/60 pcs) 1 img
Downloading DNA sequences as FASTA files in R
This is a modification of “DNA Sequence Statistics” from Avril Coghlan’s A little book of R for bioinformatics.. Most of the text and code was originally written by Dr. Coghlan and distributed under the Creative Commons 3.0 license. NOTE: There is some redundancy in this current draft that needs to be eliminated. Functions library() help...
12797 sym R (1959 sym/41 pcs)
EPAS1 Global Alignment
Global proteins aligments in R By: Ghalia Malki Adapted, edited and expanded: Nathan Brouwer under the Creative Commons 3.0 Attribution License (CC BY 3.0). Preliminaries library(compbio4all) library(Biostrings) Download sequences As we did in the previous lesson on dotplots, we’ll look at two sequences. # Download ## sequence 1: homo_fasta ...
11025 sym R (11429 sym/69 pcs)
ggplot 2
gpubr - allometric data Allometric data - classic case of regression, using logs, using non-linear model too library(compbio4all) library(ggplot2) library (ggpubr) Vocab wrapper ggplot2 ggpubr $ operator smoother continous data categorical data Learning objectives Know what a wrapper is Know the relationship between ggplot2 and ggpubr Be able...
4282 sym R (2508 sym/35 pcs) 9 img
amino acids
Key vocab proteinogenic amino acids regression model / line of best fit pI confidence intervals (CI) confidence ellipse correlation coefficient Selenocysteine and Pyrrolysine re-coding stop codons y = m*x + b slope intercept Key functions / packages ggpubr pander lm() coef() cor() round() Predict pI for an Selenocysteine and Pyrrolysine Amino...
5671 sym R (10878 sym/44 pcs) 1 img 4 tbl
FAQ GeneBank
QUESTION: How to get GeneBank Acession Numbers? Data We’ll use the “rentrez” packages (https://cran.r-project.org/web/packages/rentrez/index.html) to address this question. You’ll need to install the package with install.packages(“rentrez”) if you have not done so before, call library(“rentrez”) ###Load Packages library(rentrez) ...
1525 sym R (11304 sym/3 pcs)