We specify a pre-registered protocol for When DESeq2, edgeR, and limma-voom are applied with default settings to the same RNA-seq count matrix with an identical design formula, what fraction of genes receive discordant differential-expression calls (significant in one method but not another at FDR<0.05) and is this fraction sample-size dependent?
We specify a pre-registered protocol for Do CIBERSORT, CIBERSORTx, and quanTIseq, applied to the TCGA-BRCA RNA-seq matrix with identical inputs, agree on the tertile assignment of inferred neutrophil-to-lymphocyte ratio for individual patients? using TCGA-BRCA bulk RNA-seq expression matrix (FPKM or TPM) accessed from the GDC; patient-level barcodes and clinical file version pinned at pre-registration.
We specify a pre-registered protocol for Do Harmony, Scanorama, and scVI, applied to the same 10x Genomics PBMC 10k reference with an identical QC pipeline and a locked marker-gene reference, produce concordant cell-type labels at the top cluster level, and if not, at what fraction of cells do pairs disagree? using 10x Genomics PBMC 10k public dataset (combined from multiple publicly-released 10x PBMC runs), accessed via scanpy.