FASTQ#
A sequencing-read file containing nucleotide sequences and a quality score for each base.
Count matrix#
A gene-by-sample table of unnormalized read or fragment counts. TPM, FPKM and log-transformed values are not raw counts.
Contrast#
The comparison being estimated, including its factor, numerator and denominator. Positive log2 fold change means higher expression in the numerator.
Adjusted p-value#
A p-value adjusted for multiple testing. An FDR threshold concerns the expected proportion of false discoveries among a called set under the method assumptions; it is not the probability that one gene is false.
log2 fold change#
An effect size on a base-two logarithmic scale. +1 represents a twofold ratio; -1 represents half the expression relative to the denominator.
Covariate#
A recorded sample characteristic included in a statistical model, such as batch or donor.
PCA#
Principal component analysis: a low-dimensional view of major variation among samples. Separation is a diagnostic observation, not proof of a treatment effect.
Gene identifier#
The label used to identify a gene in a database. Symbols, Ensembl IDs and NCBI GeneIDs are different identifier namespaces.
Enrichment#
A test asking whether genes associated with a function are over-represented in a selected set or concentrated in a ranked list.
WSL2#
Windows Subsystem for Linux 2, the Linux environment used to run this application’s analysis tools on Windows.
Biological replicate#
An independently sampled biological unit. Repeated measurements or sequencing lanes of one unit do not create independent biological replicates.
Strandedness#
Whether a sequencing library preserves the orientation of the original RNA and how that orientation relates to aligned reads.
Universe#
The background genes eligible for an over-representation analysis. Its definition changes the enrichment comparison.
GSEA#
Gene set enrichment analysis, which evaluates gene sets against a ranked gene list.
GSVA#
Gene set variation analysis, used here to produce descriptive pathway-activity scores for individual samples.
Provenance#
The recorded inputs, versions, parameters and processing steps needed to establish how an output was produced.