Publications by Maia Lim
Final Portfolio: Maia Lim
Introduction This code compiles summary information about the gene EGLN1 (Egl-9 Family Hypoxia Inducible Factor 1). Links: RefSeq page: https://www.ncbi.nlm.nih.gov/gene/54583 Homologene page: https://www.ncbi.nlm.nih.gov/homologene/56936 UniProt page: https://www.uniprot.org/uniprot/F6P6J7 PDB page: NA To compare the evolutionary relationship be...
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Portfolio: Predicting AA Characteristics
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...
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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 -DOWLOAD A LIST OF REFSEQ ACCESSION NUMBERS FROM GOOGLE SHEETS -USE NA.OMIT() TO REMOVE THE NAS -USE DUPLICATED())M TO SELECT OUT ALL ISOFORMS EXCEP...
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Google Sheets Access Test
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 download a list of RefSeq accessions from a Google sheet remove the NAs using na.omit() select out all but one isoform using duplicated() Packages...
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GWAS Pie Graphs
Introduction The following graphs uses information collected by Alice B. Popejoy and Stephanie M. Fullerton from the genome-wide association studies (GWAS) Catalog. The GWAS Catalog is produced by the US National Human Genome Research Institute in partnership with the European Bioinformatics Institute where every week, curators are notified of an...
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Introduction to DotPlots
Sequence dotplots in R By: Avril Coghlan. Adapted, edited and expanded: Nathan Brouwer under the Creative Commons 3.0 Attribution License (CC BY 3.0). NOTE: I’ve added some new material that is rather terse and lacks explication. Good sources of more info: https://omicstutorials.com/interpreting-dot-plot-bioinformatics-with-an-example/ http://r...
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Adjusting Dotplot Settings
Add the necessary code to make this script function. Preliminaries Load packages library(seqinr) library(rentrez) library(compbio4all) library(Biostrings) ## Loading required package: BiocGenerics ## Loading required package: parallel ## ## Attaching package: 'BiocGenerics' ## The following objects are masked from 'package:parallel': ## ## ...
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Maia Lim: Downloading and Saving FASTA File
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...
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Knit to HTML
Default working directory Open up this .Rmd file in RStudio. In the code chunk below type getwd() and run it. “wd” means “working directory”, or where R will currently save files if you tell it to save anything. # Get the current working directory getwd() ## [1] "/Users/maialim/University of Pittsburgh/compbio2021 - mrl106" Copy and paste...
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Document
Default working directory Open up this .Rmd file in RStudio. In the code chunk below type getwd() and run it. “wd” means “working directory”, or where R will currently save files if you tell it to save anything. # Get the current working directory (where R saves things by default) getwd() ## [1] "/Users/maialim/Downloads" Copy and paste t...
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