README.md

sysbio

RNA-seq pipelines for microarray data and single cell seq

[DE,scRNA]_[DATASET]

DE- MICROARRAY DIFF EXPRESSION

1. normalize the dataset and make sure it's in log-scale
2. make sense of the PCA plot: find outliers or check for batch effect
3. Design your DE to answer general question about the data
4. run DE and perform pathway enrichment using fgsea

scRNA singel cell RNA-seq analisys

1. Preprocessing: filtering out bad cells and normalization
2. UMAP + clustering
3. Marker selection for clusters

GSE122121

In infected samples what's different with KO? Dataset:GSE122121

GSE126296

Does male and female donors respond the same way to sprint? Show unique genes and pathways for female Dataset:GSE126296