Transcriptomics toolkit covering bulk RNA-seq alignment with STAR or HISAT2, quantification with featureCounts or Salmon and kallisto, differential expression with DESeq2 or pydeseq2 and edgeR, single-cell analysis with Scanpy and AnnData, Leiden clustering and UMAP, marker genes with rank_genes_groups, batch correction with Harmony or scVI, pseudotime with PAGA and diffusion maps.
