Publications by Arhat Pradhan
Car-T Map
R Markdown This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com. When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within...
468 sym R (1261426 sym/12 pcs)
Analyzing Single Cell RNA Seq Data
#load in the libraries library(Seurat) ## Attaching SeuratObject library(tidyverse) ## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── ## ✔ dplyr 1.1.2 ✔ readr 2.1.4 ## ✔ forcats 1.0.0 ✔ stringr 1.5.0 ## ✔ ggplot2 3.4.2 �...
602 sym R (9687 sym/37 pcs) 6 img
Loading and Reading Single Cell RNA Seq Data
#load in the Seurat libraries needed library(Seurat) ## Attaching SeuratObject library(SeuratDisk) ## Registered S3 method overwritten by 'SeuratDisk': ## method from ## as.sparse.H5Group Seurat #reading in a .RDS format rds_data <- readRDS('ependymal_cells.rds') 10x CellRanger .HDF5 format hdf_data <- Read10X_h5(filename = "20k...
269 sym R (1854 sym/37 pcs)
Test
R Markdown This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com. When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks with...
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Vegan_PCA_with_msleep
Preliminaries Download the vegan package Only do this once, then comment out of the script. You may have already done this this for a previous assignment. # install.package("vegan") Load the libraries library(ggplot2) library(vegan) ## Loading required package: permute ## Loading required package: lattice ## This is vegan 2.6-2 Load the msle...
2207 sym R (3115 sym/22 pcs) 4 img
Portfolio Assignment
This Portfolio will walk you through using PCA for what I call pseudo-cluster analysis. You will also examine the PCA scores generated by PCA, how they correlate with themselves, and how they correlate to the original data features. This will help illustrate how the vectors in a biplot relate to the original data and the layout of the points...
8932 sym R (7457 sym/34 pcs) 18 img
Software Checkpoint: vcfR
This code checkpoint will make sure that you can load .vcf files on your computer. You will also review vocab and concepts related to .vcf files and SNPs. You will need to load an analyze a .vcf file on the final exam. Make notes on all of this material and include it on your notes sheet. Learning objectives This material will appear on the f...
5541 sym R (4030 sym/25 pcs)
Software Checkpoint - Setting a working directory and loading data
Learning objectives All of this material will appear on the exam. Take notes on the workflow, functions, and concepts. Main objectives By the end of this lesson you will know how to.. set a working directory in RStudio confirm the location of the working directory with getwd() confirm a file is present with and list.files(pattern = ...) load...
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Portfolio: Working with SNP files 1 - loading and transposing VCF files
NOTE - before you begin, make sure your WORKING DIRECTORY is set to the location of the .vcf file being used. Learning objectives All of this material will appear on the exam. Take notes on the workflow, functions, and concepts. Set a working directory and confirm a file is present with getwd() and list.files(pattern = ...) Know what it me...
4845 sym R (9476 sym/42 pcs)
Software Checkpoint: Loading your VCF file into R
R Markdown This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com. When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks with...
420 sym R (176456 sym/8 pcs)