Publications by Xiaohan Xu
Portfolio: Investigating your focal gene for the presence of repeats - Xiaohan Xu
Change the XXXXX of the title to your gene name. Change the names and text appropriately to reflect your gene / protein. Add the necessary code to make this script functional. Download the PROTEIN sequence of your gene. Adapting the code below, make 2 grids of 4 plots (8 plots total) exploring different settings for window size and the match thre...
1609 sym R (6068 sym/35 pcs) 5 img
Portfolio - Pairwise alignment
Global proteins aligments in R By: Avril Coghlan. 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: Q9CD83 lep...
11066 sym R (13879 sym/61 pcs)
Review Portfolio - downloading, cleaning, and aligning data
The goal of this exercise is to make you familiar with how to download data from Google Sheets and to briefly review some key concepts R functions and coding concepts. We’ll do the following things (TODO: MAKE YOUR OWN OUTLINE) Packages ## Google sheets download package # comment this out when you are done # install.packages("googlesheets4") l...
3300 sym R (17552 sym/122 pcs) 1 img
Xiaohan Xu Portfolio - Predicting amino acid chemistry using regression models
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...
5650 sym R (6547 sym/24 pcs) 1 img 3 tbl
Final portfolio xix62
R Markdown This code compiles summary information about the gene DOCK3. This gene is specifically expressed in the central nervous system (CNS). It encodes a member of the DOCK (dedicator of cytokinesis) family of guanine nucleotide exchange factors (GEFs). This protein, dedicator of cytokinesis 3 (DOCK3), is also known as modifier of cell adhesi...
1397 sym R (48305 sym/127 pcs) 6 img 3 tbl