Aim of the Project: To find a scientific paper which has used R tool for analysis. Once we get the paper, we need to: 1.Extract the relevant data sets from the paper in an excel file. 2.Write a R...

1 answer below »
I have attached the document and I have explained the key points in the chat box.Flexible with the deadlines


Aim of the Project: To find a scientific paper which has used R tool for analysis. Once we get the paper, we need to: 1.Extract the relevant data sets from the paper in an excel file. 2.Write a R script for these data to reproduce same results like in the paper. I have few papers at my end, topic assigned to me is related to ovary cancer. Please let me know if you could select any of the paper from below and help in doing steps 1 and 2. 1.https://www.nature.com/articles/s41598-019-45165-4 MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature 2. https://pubmed.ncbi.nlm.nih.gov/23550061/ CuratedOvarianData: clinically annotated data for the ovarian cancer transcriptome 3. https://pubmed.ncbi.nlm.nih.gov/31940494/ Mouse Ovarian Cancer Models Recapitulate the Human Tumor Microenvironment and Patient Response to Treatment 4. https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(20)30364-9/fulltext BET, SRC, and BCL2 family inhibitors are synergistic drug combinations with PARP inhibitors in ovarian cancer 5. https://www.nature.com/articles/s41467-019-11862-x The molecular origin and taxonomy of mucinous ovarian carcinoma 6. https://www.nature.com/articles/s41467-020-15951-0 Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer Note: Papers might look very technical, we can pick up simple things and reproduce a simple analysis from any of the paper. Aim is learning how to rewrite a science paper in R. Else any other suggestion would be helpful. If the tutor finds the paper difficult, I am open to the tutor's suggestions to work on a less complicated paper. But would be great if we can work on something related to ovary cancer research or we can discuss if everything looks difficult, to find a simple cancer paper. Please check this link below and prepare the heat map in the R studio for the data attached in the excel. https://jcoliver.github.io/learn-r/009-expression-heatmaps.html The heatmap should look like this: It has been taken from the paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6963791/
Answered 28 days AfterFeb 03, 2021

Answer To: Aim of the Project: To find a scientific paper which has used R tool for analysis. Once we get the...

Mohd answered on Feb 12 2021
144 Votes
Untitled
Untitled
-
04/02/2021
#if (!requireNamespace("BiocManager", quietly = TRUE))
#install.packages("BiocManager")
#BiocManager::install("ComplexHea
tmap")
library(ComplexHeatmap)
## Loading required package: grid
## ========================================
## ComplexHeatmap version 2.6.2
## Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
## Github page: https://github.com/jokergoo/ComplexHeatmap
## Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
##
## If you use it in published research, please cite:
## Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
## genomic data. Bioinformatics 2016.
##
## This message can be suppressed by:
## suppressPackageStartupMessages(library(ComplexHeatmap))
## ========================================
#BiocManager::install("dendextend")
library(dendextend)
##
## ---------------------
## Welcome to dendextend version 1.14.0
## Type citation('dendextend') for how to cite the package.
##
## Type browseVignettes(package = 'dendextend') for the package vignette.
## The github page is: https://github.com/talgalili/dendextend/
##
## Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
## Or contact:
##
## To suppress this message use: suppressPackageStartupMessages(library(dendextend))
## ---------------------
##
## Attaching package: 'dendextend'
## The following object is masked from 'package:stats':
##
## cutree
#install.packages("corrplot")
library(corrplot)
## corrplot...
SOLUTION.PDF

Answer To This Question Is Available To Download

Related Questions & Answers

More Questions »

Submit New Assignment

Copy and Paste Your Assignment Here