Tag: z-score

r – RNA-Seq Data Heatmap: Is it necessary to do a log2 transformation of RPKM values before doing the Z-score standardisation?

I am making a heatmap using RNA-Seq data in R. The heatmap shows gene expression values (RPKM) in different brain regions. I have the following code: library(tidyverse) library(pheatmap) library(matrixStats) read_csv(“prenatal_heatmap_data.csv”) -> all_data all_data %>% column_to_rownames(“Brain Region”) -> heatmap_data heatmap_data %>% pheatmap() Which generates the following heatmap: I want to do…

Continue Reading r – RNA-Seq Data Heatmap: Is it necessary to do a log2 transformation of RPKM values before doing the Z-score standardisation?

AttCRISPR: a spacetime interpretable model for prediction of sgRNA on-target activity | BMC Bioinformatics

Dataset The dataset we used for training, validation and testing is the DeepHF dataset [17]. We extracted 55604, 58617, 56888 sgRNAs with activity (represented by insertion/deletion (indel)) for WT-SpCas9, eSpCas9(1.1) and SpCas9-HF1, respectively, from its source data, and use the same partition method to divide train set and test set….

Continue Reading AttCRISPR: a spacetime interpretable model for prediction of sgRNA on-target activity | BMC Bioinformatics