pirl-unc / tcrsift

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• docs/readme-session-features
• add-enrichment-branch
• cedar-autodownload
• check-synth-dupsc-fix
• chore/246-no-assemble
• chore/drop-single-chain-nt-contig
• chore/fast-default-tests
• chore/fix-anndata-warnings-at-source
• chore/remove-dead-code
• chore/remove-olga-sonia
• chore/silence-thirdparty-warnings
• ci/parallel-tests-single-cov
• close-120-trac-polymorphism-visibility
• codex/fix-logistic-filtering-and-optional-deps
• combined-pdf-fixes
• feat-allele-reasons-and-novel-detection
• feat-codon-opt-stops-assembly-cols
• feat-contig-aware-constant-nt
• feat/161-expansion-qc
• feat/161-sample-qc
• feat/161-sort-consistency
• feat/2.71.0-plot-followups
• feat/2.72.0-leader-kozak-qc
• feat/2.73.0-hregion-trim
• feat/2.74.0-germline-leaders
• feat/2.75.0-germline-columns
• feat/2.76.0-putative-indel-variants
• feat/2.77.0-leader-plot
• feat/2.78.0-report-outputs
• feat/adaptive-signature-cutoff
• feat/annotate-db-metadata
• feat/annotate-pgen-ppost-default
• feat/annotated-report
• feat/antigen-response-signature
• feat/attribution-176
• feat/baseline-markers-config
• feat/bundle-ppost-source
• feat/cellranger-dir-124
• feat/clone-sample-long-csv
• feat/cohort
• feat/consistent-condition-ordering
• feat/constant-allele-fidelity-187
• feat/contextual-signatures
• feat/data-cache
• feat/donor-method-aggregations
• feat/donor-method-filters
• feat/donor-method-foundation
• feat/donor-sharing-bucketing
• feat/dual-alpha-cofraction-visibility
• feat/extended-assembly-qc
• feat/fdr-scope
• feat/finish-select-report-122-123
• feat/freq-prism-grid-207
• feat/freq-tiebreak
• feat/funnel-qc-signatures-batch
• feat/method-overlap-and-recovery
• feat/new-issues-batch
• feat/orthogonal-dual-split-181
• feat/orthogonal-split-181
• feat/per-method-rankings
• feat/pgen-publicness
• feat/prism-nan-guard
• feat/prism-per-condition-recipe
• feat/prism-route-193
• feat/rehydrate-obs
• feat/rename-selection-rule
• feat/report-bundle-123
• feat/run-emits-per-sample-tier
• feat/run-selected-clones
• feat/select-command-122
• feat/selected-clones-report-188
• feat/selected-report-cover-combine-202
• feat/selection-context-plots
• feat/selection-refinements
• feat/selection-routes
• feat/seqprob-kmer-tcrpeg
• feat/set-overlap-upset-208
• feat/signature-methods
• feat/specificity-and-output-polish
• feat/surface-viral
• feat/synthesis-hazard-qc-206
• feat/til-overlap-per-donor
• feat/timepoint-apc-aggregations
• feat/timepoint-apc-filters
• feat/timepoint-apc-foundation
• feat/warn-low-qc-pass-rate
• feature/43-remaining-plots
• feature/annotation-plots-phase-b
• feature/antigen-canonical-symbols
• feature/iedb-epitope-canonical-names
• feature/rank-family-plots
• feature/structured-db-annotation
• fix-100-canonical-constants-from-pyensembl
• fix-105-alpha-junction-residue
• fix-107-validator-junction-prepend
• fix-109-plot-labels
• fix-113-multi-allele-option-d
• fix-296-annotations-shadowing
• fix-56-match-confidence-score
• fix-57-levenshtein-match
• fix-88-89-90-jc-parity-cross-source
• fix-91-nt-frame-orf
• fix-99-tier-abundance-specificity-split
• fix-allele-audit-position-denominator
• fix-load-samples-memory
• fix/129-qc-warnings-load-bearing
• fix/141-142-signature-recompose
• fix/143-olga-ppost
• fix/144-scoring-hardening
• fix/145-reproducibility-map
• fix/149-insilico-filter
• fix/150-allele-mapping
• fix/230-deterministic-serialization-order
• fix/235-junction-residue-and-contig-case
• fix/235-junction-seam-qc-guard
• fix/242-traj-junction-map
• fix/aggregate-clonotypes-categorical
• fix/apply-qc-filter
• fix/assemble-constant-region-and-pdf-column-order
• fix/audit-high-bugs
• fix/audit-polish
• fix/cache-test-isolation
• fix/cli-config-and-contigs-195-196
• fix/clone-sample-long-complete-numerator
• fix/csc-concat-on-disk
• fix/dual-alpha-dominance-gate-198
• fix/dual-alpha-variant-contig-ids
• fix/fidelity-fail-closed-and-dual-alpha
• fix/h5ad-dtype-and-bug-cleanup
• fix/iedb-v3-parser
• fix/keep-unanimous-substitution-leaders
• fix/method-recovery-populated-tier
• fix/min-cd3-gate
• fix/multi-db-download
• fix/pandas-warnings-and-cdr3ab-pairing
• fix/pdf-text-formatting
• fix/plot-vector-output
• fix/qc-config-footguns
• fix/representative-vdj-cdr3-consistency-184
• fix/run-default-sheet-contigs-201
• fix/sanity-check-batch
• fix/skip-none-metadata
• fix/uns-sample-sheet-h5ad
• fix/vdjdb-loader-issues
• fix/warn-filter-noops
• freq-heatmap-readability
• germline-region-report
• harden/load-path-coverage
• het-aware-leaders-274
• hotfix-1.0.1-python39
• hygiene-redundant-imports
• main
• native-qc-battery-279
• perf/marker-extraction
• prune-dumb-tests
• qc-check-synth-283
• qc-warnings-schema-278
• recode-vdj-hazards
• refactor/prism-unification
• run-provenance-stamping
• selected-annotation-and-freq-heatmap
• selection-per-condition-columns
• speedup/test-dpi-and-agg-backend
• vregion-allele-fix
• vregion-framework

Build # 25711264988

Build Type

Pull #34

github

Committed by web-flow

Commit Message

Merge a337418b2 into ac9a4137e

Pull Request Pull Request #34: Document tcrsift data, --fdr-scope, and multi-method outputs in README

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