Author: gene_x

Abstract: Plot Chao1 richness estimator, Observed OTUs, Shannon index, and Phylogenetic diversity. Regroup together samples from the same group. [![alpha_diversity1_resized](/static/plotting_alpha_diversities/

Author: gene_x

Abstract: [](/static/rnaseq_skin_organoid_herpesvirus/PCA_3D_cropped.png "PCA_3D_cropped") [![normalization_small]

Author: gene_x

Abstract: Normalization methods for RNA-seq data 1. DESeq (RLE - Relative Log Expression): - Goal: To normalize for differences in library size and distribution of read counts. - Method: Uses a medi

Author: gene_x

Abstract: 3. import data and pca-plot # Import the required libraries library("AnnotationDbi") library("clusterProfiler") library("ReactomePA") library(gplots) l

Author: gene_x

Abstract: 1. TODO on sage check the alignment of the reads to the annotation which sent from Munich is very bad, using the reference X14112 instead, find the CMV-GFP in the genome. Using alignment to detec

Author: gene_x

Abstract: [](/static/chrHsv1_genomic_annotation/chrHsv1_s17

Author: gene_x

Abstract: 1. Verwenden Sie Mamba: Mamba ist eine schnellere Alternative zu Conda und kann Pakete und deren Abhängigkeiten schneller auflösen und installieren. Sie können es mit 'conda install mamba' installiere

Author: gene_x

Abstract: A common tool to utilize RNAseq data to correct or enhance a reference genome, especially for viruses, is StringTie. This tool is primarily designed for transcript assembly and quantification based on

Author: gene_x

Abstract: 1. Herpes Simplex Virus 1 (HSV-1) and Herpes Simplex Virus 2 (HSV-2) are closely related viruses that belong to the Herpesviridae family. Both viruses have a similar genomic structure but differ in th

Author: gene_x

Abstract: 0. nextflow (rnaseq) [jhuang@sage Data_Denise_LT_RNAseq]$ nextflow run rnaseq/main.nf --input samplesheet.csv --outdir results_GRCh38 --genome GRCh38 -profile test_full -resume --max_memor