R-loopReScore

R-loopReScore is an online tool that quantifies R-loop regulatory states from transcriptomic expression profiles, capturing both overall regulator activity and the balance between R-loop-promoting and R-loop-suppressing regulation.

Species

Homo sapiens

Study type *

Gene identifier *

Expression matrix *

No file selected

Please upload a tab-delimited expression matrix with a header. The first column should contain gene identifiers (Entrez ID or Ensembl ID), and the remaining columns should contain expression values for individual samples or cells. Ensembl or Entrez IDs are recommended. For bulk RNA-seq, please provide normalized gene expression values, with all samples processed using the same normalization procedure. For single-cell RNA-seq, please provide non-negative, log-normalized expression values generated by library-size normalization followed by natural-log log1p transformation.

Download scRNA-seq example Download bulk RNA-seq example

Score Interpretation

RloopReScore	A direction-aware score reflecting the relative dominance of R-loop-promoting regulators (T_promote) versus R-loop-suppressing regulators (T_suppress), normalized against expression-matched background activities for the promoting (B_randomⁿ) and suppressing (B_random^m) regulator groups. Positive values indicate a shift toward R-loop-promoting regulation, whereas negative values indicate a shift toward R-loop-suppressing regulation. Values near zero indicate no strong directional imbalance. $T_{promote} = \sum_{i \in G_{promote}} x_{i}$ $T_{suppress} = \sum_{i \in G_{suppress}} x_{i}$ $RloopReScore = \frac{(T_{promote} - T_{suppress}) - mean (B_{random}^{n} - B_{random}^{m})}{sd (B_{random}^{n} - B_{random}^{m})}$
OverallScore	A direction-independent score reflecting the overall expression activity of all R-loop regulators (T_obs) relative to expression-matched background genes (B_random). Higher values indicate globally elevated R-loop regulator activity, regardless of whether the regulators promote or suppress R-loop formation. $T_{obs} = \sum_{i \in G_{all}} x_{i}$ $B_{random}^{k} = \sum_{i \in G_{random}^{k}} k_{i}$ $OverallScore = \frac{T_{obs} - mean (B_{random}^{k})}{sd (B_{random}^{k})}$

RloopReScore

A direction-aware score reflecting the relative dominance of R-loop-promoting regulators (T_promote) versus R-loop-suppressing regulators (T_suppress), normalized against expression-matched background activities for the promoting (B_randomⁿ) and suppressing (B_random^m) regulator groups. Positive values indicate a shift toward R-loop-promoting regulation, whereas negative values indicate a shift toward R-loop-suppressing regulation. Values near zero indicate no strong directional imbalance.

T_{promote} = \sum_{i \in G_{promote}} x_{i}

T_{suppress} = \sum_{i \in G_{suppress}} x_{i}

RloopReScore = \frac{(T_{promote} - T_{suppress}) - mean (B_{random}^{n} - B_{random}^{m})}{sd (B_{random}^{n} - B_{random}^{m})}

OverallScore

A direction-independent score reflecting the overall expression activity of all R-loop regulators (T_obs) relative to expression-matched background genes (B_random). Higher values indicate globally elevated R-loop regulator activity, regardless of whether the regulators promote or suppress R-loop formation.

T_{obs} = \sum_{i \in G_{all}} x_{i}

B_{random}^{k} = \sum_{i \in G_{random}^{k}} k_{i}

OverallScore = \frac{T_{obs} - mean (B_{random}^{k})}{sd (B_{random}^{k})}

Result Display

After submission, you can preview and download all analysis results.