This page walks through how to prepare inputs and run each tool. Use the examples below as templates, then adapt them to your data to get reliable results.
Upload a raw count matrix with one gene per row and samples in columns. Make sure sample names match your group labels exactly, and keep counts untransformed (no TPM/RPKM).
Gene Sample_A1 Sample_A2 Sample_B1 Sample_B2
BRCA1 123 118 95 102
BRCA2 45 51 38 41
TP53 300 289 275 290
EGFR 210 198 165 172Provide a ranked gene list with fold change or logFC values. This should be ordered in descending order (highest logFC at the top) so enrichment tools interpret the direction correctly.
Gene logFC
MYC 2.35
STAT3 1.88
VEGFA 1.42
EGFR 1.10
BRCA1 0.85
BRCA2 0.41
TP53 0.10Supply Ensembl (ENSG) or Entrez IDs, one per line. Remove version suffixes like ".1" from Ensembl IDs and select the correct organism to avoid mismatches.
GeneID
ENSG00000187243
ENSG00000171316
ENSG00000213071
ENSG00000237440
ENSG00000111305
Use an expression matrix with genes in rows and samples in columns. The tool expects normalized values (such as log2 TPM) and gene sets in GMT format.
Gene Sample_1 Sample_2 Sample_3
TP53 7.2 7.5 6.9
BRCA1 5.1 5.3 4.9
BRCA2 4.6 4.9 4.2
EGFR 6.0 5.7 5.5
MYC 8.2 8.0 7.8For the FASTQ-to-counts workflow tutorial, click here.