R practice in Computational Biology

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• Count the Usable Bases

  A field sequencer exported gaps and unknowns. Count only canonical DNA bases before the team compares samples.

  sequence-qc. Free room.

• Find Every Motif

  A curator needs every overlapping occurrence of a short motif, including repeats that share residues.

  motif-search. Free room.

• Read the Coding Frame

  A gene model needs the number of complete codons in a sequence. Return complete triplets and leave trailing bases unclaimed.

  coding-sequence. Free room.

• Summarize Library Depth

  A sequencing run has one count column per sample. Return the named library totals without losing sample identity.

  count-matrix. Free room.

• Balance Assay Blocks

  RNA and protein blocks have different feature counts. Center each block and scale it to unit Frobenius norm.

  block-scaling. Account access required.

• Measure Sequence Divergence

  Two aligned sequences disagree at some usable positions. Report the mismatch fraction without counting gaps.

  sequence-distance. Account access required.

• Merge Domain Hits

  A domain scan emitted overlapping intervals. Merge them into non-overlapping one-based closed regions.

  intervals. Account access required.

• Rank Variable Genes

  An assay needs a deterministic shortlist. Rank gene rows by variance and use gene name to settle ties.

  feature-ranking. Account access required.

• Audit the Sample Map

  A multi-omic cohort map may omit assay samples. Return every missing assay::sample key.

  sample-identity. Account access required.

• Bootstrap a Clade

  Replicate trees list their supported splits. Calculate target support using successful replicates only.

  bootstrap-support. Account access required.

• Keep Subjects Together

  Repeated samples must never cross validation folds. Assign deterministic folds by unique subject.

  grouped-validation. Account access required.

• Score a Protein Candidate

  A review queue needs a transparent evidence score. Reward assays, reciprocal homology, and motifs, then subtract conflicts.

  evidence-scoring. Account access required.

• Audit Subgroup Loss

  A model performs unevenly across groups. Return the largest difference in mean loss while keeping every group in the audit.

  subgroup-audit. Account access required.

• Correct Hidden Substitutions

  Observed divergence misses repeated substitutions. Apply the Jukes-Cantor correction and mark saturation unavailable.

  evolution-model. Account access required.

• Link Omic Views Cautiously

  Two subject-aligned features may move together. Align subject names and return their Pearson correlation.

  cross-omic-association. Account access required.

• Fit the Molecular Clock

  Sampling dates and root-to-tip distances need an aligned regression. Return the slope without trusting vector order.

  clock-regression. Account access required.

• Challenge Protein Claims

  A protein candidate has coverage, conflicts, and assay support. Return the narrowest defensible review tier.

  bounded-interpretation. Account access required.

• Detect Cohort Leakage

  A preprocessing log lists subjects used to fit each transform. Flag any held-out subject appearing in a fit.

  leakage-audit. Account access required.

• Publish the Evidence Dossier

  A project is ready only if identity, leakage, coverage, and validation checks all pass. Return the highest-priority status.

  evidence-dossier. Account access required.

• Reconstruct the First Branch

  A distance matrix needs a deterministic first average-linkage merge. Return the lexical pair among tied minima.

  tree-reconstruction. Account access required.