Guidelines for Final Lab Report Guidelines for Final Lab Report Course: 01:447:303 Author: Prof. Premal Shah Objective: The primary objective of the finals lab report is to apply R programming skills...

apply R programming skills to perform comparative analyses of genomic features of any two organisms. Genome data can be found free at Ensembl.org


Guidelines for Final Lab Report Guidelines for Final Lab Report Course: 01:447:303 Author: Prof. Premal Shah Objective: The primary objective of the finals lab report is to apply R programming skills to perform either (i) comparative analyses of genomic features of any two organisms or (ii) differential gene expression and functional enrichment analyses using RNA-seq data. • Submission format: The finals project report will be submitted as a single R HTML Notebook (*.nb.html) file. Any additional files or datasets needed to execute the code can be submitted as a single ZIP file. • Structure: The report will contain the following sections a. Title: The authors will create a descriptive title for their report and list the names of all authors. b. Introduction: The authors will justify their choice of organisms & the nature of genomic comparisons or choice of RNA-seq data. (1—2 paragraphs) c. Code: Before each code chunk the authors will describe what data/ analyses/plot that particular chunk will generate. i. Comments: The R code will be extensively commented. Lack of clear comments will lead to loss of points. ii. Plots: The report will contain 3 plots each describing unique analyses. iii. Statistical tests: The report will contain the code for 3 statistical analyses. The authors will also justify their choice of a particular statistical test. Note: Statistical tests can be associated with plots but they don’t have to. The statistical tests can be separate from the visualization. iv. Inferences: The authors will provide descriptive statements indicating what inferences were drawn based on their plot/statistical analyses. d. Summary: At the end of the report, the authors will summarize their findings in a summary paragraph. 
 Points: Total 50 points • Title — 1 pt • Introduction — 5 pt • Analyses — a. Each plot — code (3pt) + comment (1pt) + accuracy/aesthetics (1pt) = 15 pt. b. Each statistical test — code (3pt) + comment (1pt) + justification (1pt) = 15 pt c. Each inference — 3pt = 9 pt • Summary — 5 pt OK, so in the guidelines (assignment) that I sent to you, there are 2 options either (i) comparative analyses of genomic features of any two organisms or (ii) differential gene expression and functional enrichment analyses using RNA-seq data I would like to do the first one for which the .fa file was sent i can give you another .fa file (2 of them) one has data on BosMutus (wild yak) and another has data on BosTaurus (cattle), both data are on Hypoxia in both organisms. I have run some code on that These are the packages that need to be installed: library("Biostrings") library("rtracklayer") library("GenomicRanges") library("seqinr") library("ggplot2") library("ShortRead") library("psych") library("BiocFileCache") library("dbplyr") library("dplyr") library("reshape") library("DESeq2") library("ggpubr") This is 1st code: BosMutus_fasta <- read.fasta(file.choose())="" bosmutus_fasta="" bosmutus_seq=""><- bosmutus_fasta$jh882107.1="" head(bosmutus_seq)="" table(bosmutus_seq)="" bosmutus_fasta=""><- read.fasta(file.choose())="" bosmutus_fasta="" bosmutus_seq=""><- bosmutus_fasta$jh882107.1="" head(bosmutus_seq)="" table(bosmutus_seq)="" bostaurus_fasta=""><- read.fasta(file.choose())="" bostaurus_fasta="" bostaurus_seq=""><- bostaurus_fasta$`19` head(bostaurus_seq) table(bostaurus_seq) c. code: before each code chunk the authors will describe what data/ analyses/plot that particular chunk will generate. i. comments: the r code will be extensively commented. lack of clear comments will lead to loss of points. ii. plots: the report will contain 3 plots each describing unique analyses. iii. statistical tests: the report will contain the code for 3 statistical analyses. the authors will also justify their choice of a particular statistical test. note: statistical tests can be associated with plots but they don’t have to. the statistical tests can be separate from the visualization. iv. inferences: the authors will provide descriptive statements indicating what inferences were drawn based on their plot/statistical analyses. d. summary: at the end of the report, the authors will summarize their findings in a summary paragraph. section c & d  need help with statistical tests.... i actually ran one already checking similarily between 2 gene sequences of hypoxia in both organisms i need 2 more statistical tests and 2 more plots bostaurus_fasta$`19`="" head(bostaurus_seq)="" table(bostaurus_seq)="" c.="" code:="" before="" each="" code="" chunk="" the="" authors="" will="" describe="" what="" data/="" analyses/plot="" that="" particular="" chunk="" will="" generate.="" i.="" comments:="" the="" r="" code="" will="" be="" extensively="" commented.="" lack="" of="" clear="" comments="" will="" lead="" to="" loss="" of="" points.="" ii.="" plots:="" the="" report="" will="" contain="" 3="" plots="" each="" describing="" unique="" analyses.="" iii.="" statistical="" tests:="" the="" report="" will="" contain="" the="" code="" for="" 3="" statistical="" analyses.="" the="" authors="" will="" also="" justify="" their="" choice="" of="" a="" particular="" statistical="" test.="" note:="" statistical="" tests="" can="" be="" associated="" with="" plots="" but="" they="" don’t="" have="" to.="" the="" statistical="" tests="" can="" be="" separate="" from="" the="" visualization.="" iv.="" inferences:="" the="" authors="" will="" provide="" descriptive="" statements="" indicating="" what="" inferences="" were="" drawn="" based="" on="" their="" plot/statistical="" analyses.="" d.="" summary:="" at="" the="" end="" of="" the="" report,="" the="" authors="" will="" summarize="" their="" findings="" in="" a="" summary="" paragraph.="" section="" c="" &="" d=""  need="" help="" with="" statistical="" tests....="" i="" actually="" ran="" one="" already="" checking="" similarily="" between="" 2="" gene="" sequences="" of="" hypoxia="" in="" both="" organisms="" i="" need="" 2="" more="" statistical="" tests="" and="" 2="" more="">