Sync wiki: 3-route flow diagram (plot / genome browser / analysis)
Sync wiki: per-section output crops in Mapping; auto linkout + Static/Interactive table in Plotting; public viewer source in Python-API; two-route flow diagram
Sync wiki: clean node-based flow diagram
Sync wiki: harmonized flow diagram
Sync wiki from main: single --out/--engine plotting, viewer GIFs, ASCII prose, updated benchmarks/figures
fetch Zenodo-only wording; plain Windows note; drop Docker/smoke; consolidate benchmark tables (1M threads×batch grid); custom-GTF stdout-only
Updated Home (markdown)
Fixed Typos
Fix index docs: Home fetch path, drop bogus human-v115 row, 298 MB index, Plotting segments import - Home quickstart: 'fetch human --out human.idx' so the next map step's --index human.idx actually resolves (fetch defaults to ~/.cache). - Drop the fabricated 'human-v115 / ensembl_v15_human.idx' pre-built row (no such Zenodo target). - Performance: human GENCODE index is ~298 MB, not 128 MB. - Plotting: import _segments_from_dataframe from prot2exon.plot instead of the broken p2e.plot.<attr> path.
Restructure wiki into a sequential 7-section workflow Install -> Building an index -> Mapping -> Plotting -> Tutorials and notebooks -> Performance and benchmarking -> Reference. Merge the old scattered pages (Genome-onboarding + Custom-proteins -> Index; Output-modes + Input-format -> Mapping; Performance-and-RAM + Validation + Benchmarks -> Performance and benchmarking); drop the standalone Quickstart and CLI-reference. Update all CLI to the four-command form (index / map / fetch / plot) and the fetch-defaults-to-Zenodo model. Sidebar lists each section's subsections.
Initial wiki — 17 pages mirrored from main repo wiki/
Initial Home page