Transcriptomics_note

Tutorial and course

• NIH/NCI: Bioinformatics Training and Education Program by BioStar
• Computational Genomics with R

Downstream tools

• Biomedical Knowledge Mining using GOSemSim and clusterProfiler
• Rafael Irizarry lab
• Saez-Rodriguez Group
• X. Shirley Liu lab
• Ma'ayan lab
• Tommy tweet

P-value distribution issue

• Genes with low counts interfere with the p-value distribution, so removing those genes and re-observe the distribution. Ref

Genes selection

• RNA-seq included many types of RNA (GENETYPE). We typically want protein-coding genes, so we need to filter only those using the annotation package to identify it.