BEATS

The BEATS modules provide means to tackle Batch Effects in multi-sample transcriptome data sets. BEATS stands for Batch Effect Antagonist Transcriptomes Synchronization

compute_tpm.py

Used to TPM (transcript per million reads) normalize a raw Gene Expression matrix.

assemble_GE_matrix.R

Used to assemble a gene expression matrix [nb_gene x nb_samples] from star readcounts output files

run_limma.R

Used to run a limma DEGanalysis on a GE matrix (tpm transformed)

run_deseq.R

Used to run a DESEQ2 DEGanalysis on a GE matrix (unnormalized)