Publications by Author: Joy Nyaanga
ATAC-seq sample report
Background Workflow method Output files Summary Visualizations: Volcano Plots Gene set enrichment analysis Conclusion Background ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a cutting-edge technique in genomics that allows researchers to explore the accessibility of chromatin regions within a genome. Chromatin accessib...
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easyXpress
A walk-through of easyXpress Author: Joy Nyaanga 05 May 2021 Introduction easyXpress is an R package to read, process, and analyze C. elegans microscopy data processed with CellProfiler’s WormToolbox. It provides functions for reading, flagging, and pruning data. Additional functionalities are available for visualizing plate information, well i...
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Nyaanga_finalpresentation
Introduction Learning objectives Project questions Analysis using Bowtie & DESeq2 Step 1. Trimming, mapping, and indexing Bowtie: FastQ -> Bam/Bai Step 2. Bam -> Granges Generate count matrix Step 3. PCA Perform PCA on data from both groups combined Split data into research groups and rerun PCA Step 4. Run DESeq2 on groups separately An...
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Data_Visualization
Today is our last day of our basic R introduction. We will be plotting our data using ggplot2! Load Packages and Read Data Similar to the last few weeks, let’s begin by loading the packages that we will need today. library(tidyverse) library(here) Great. Now I will read in the data the same way we’ve done before. #list files files <- list.fi...
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Tidy&Process
Today we are going to tidy and process our data into a suitable format for future plotting. I will break down the steps for manipulating and tidying the data into 6 main steps below. Load Packages and Read Data Similar to last week, let’s begin by loading the packages that we will need today. library(tidyverse) library(here) Great. Now I will ...
6448 sym R (1577 sym/13 pcs) 8 tbl
Reading_Data
Load Packages Lets start by loading in information from necessary packages: Notice that the here package is indicating that I am in my folder under Joy_worm_images. library(tidyverse) ## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 �...
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