Add 7.0 releases page

Author: susannasiebert

docs/index.rst

@@ -154,11 +154,6 @@ ____________
   files has been renamed to ``Index`` in order to ensure consistency between
   these and other tools.
 
-Bugfixes
-________
-
-* placeholder
-
 Past release notes can be found on our :ref:`releases` page.
 
 To stay up-to-date on the latest pVACtools releases please join our :ref:`mailing_list`.

docs/releases/7_0.rst

@@ -0,0 +1,97 @@
+Version 7.0
+===========
+
+Version 7.0.0
+-------------
+
+This is a major version release. Please note that pVACtools 7.0 is not guaranteed to be
+backwards-compatible and certain changes could break old workflows.
+
+New Tools
+_________
+
+* pVACseq now has the option of running machine learning (ML)-based neoantigen prioritization
+  predictions. The ML predictor uses a trained random forest model to predict whether neoantigen
+  candidates in the aggregated report should be evaluated as "Accept", "Reject", or "Pending"
+  based on a comprehensive set of features derived from binding affinity predictions, expression
+  data, and variant characteristics. The ML predictor can be enabled by adding the ``--run-ml-predictions``
+  parameter to a pVACseq run. More details can be found in the :ref:`output file documentation <ml_prediction_output>`,
+  the :ref:`vignette <pvacseq_vignette>`.
+
+New Features
+____________
+
+- pVACtools now supports multiple additional prediction algorithms:
+
+  - MixMHCpred (class I binding score and percentile)
+  - MixMHC2pred (class II binding score and percentile)
+  - PRIME (class I immunogenicity score and percentile)
+  - TLBind (class I binding score and class I presentation score)
+  - TLImm (class I immunogenicity score)
+  - ImmuScope (class II immunogenicity score)
+
+- In order to support a more comprehensive evaluation of candidates, aggregate binding, presentation,
+  and immunogenicity information is now available in the final reports and is used to filter, prioritize,
+  and tier candidates:
+
+  - Best and median binding percentiles, presentation percentiles and
+    immunogenicity percentiles are now calculate in the all_epitopes.tsv,
+    filtered.tsv, and aggregated.tsv files in addition to the previously
+    available combined percentiles that were aggregating percentile ranks
+    over all prediction algorithms regardless of algorithm type.
+  - Three new parameters - ``--binding-percentile-threshold``, ``--presentation-percentile-threshold``,
+    and ``--immunogenicity-percentile-threshold`` replace the old
+    ``--percentile-threshold``. These three new thresholds have been updated
+    to use a default of 2.0 instead of not having a default. This means that
+    filtering and tiering will now by default include evaluation of binding,
+    presentation, and immunogenicity percentiles.
+  - The aggregate report ``PoorBinding`` tier now evaluates the IC50
+    binding affinity as well as the binding percentile. Candidates failing
+    either threshold (when a ``conservative`` ``--percentile-threshold strategy`` is
+    selected, default) or both thresholds (when a ``exploratory``
+    ``--percentile-threshold-strategy`` is selected) will be binned in this
+    tier when all other evaluation criteria are passed.
+  - Two new tiers, ``PoorPresentation`` and ``PoorImmunogenicity``, are
+    added to bin candidates that failed the
+    ``--presentation-percentile-threshold`` or
+    ``--immunogenicity-percentile--threshold``, respectively, when all other
+    evaluation criteria are passed.
+  - pVACvector has been updated to work on the binding percentile instead of the
+    combined percentile. The corresponding parameter has been renamed to
+    ``--binding-percentile-threshold`` with a new default of 2.0. The junction
+    output file header recording each junction's binding percentile has been
+    updated from ``percentile`` to ``binding_percentile`` to reflect this change.
+  - pVACview has been updated to display more information regarding
+    immunogenicity and presentation scores.
+  - pVACtools runs that do not use a binding predictor would previously skip
+    the binding filter, top score filter, and the aggregate report creation. These
+    steps will now be run.
+
+- The ``--top-score-metric2`` has been updated for sorting candidates and
+  determining the criteria for selecting the Best
+  Peptide (in the aggregate report) and top candidate (in the top score
+  filter). It is now a list of criteria to consider. All listed criteria are
+  assigned a rank and the sum of those ranks is used. By default both the IC50
+  (``ic50``) and the combined percentile (``combined_percentile``) are used.
+  Other allowed values are the binding percentile (``binding_percentile``),
+  the presentation percentile (``presentation percentile``), and the
+  immunogenicity percentile (``immunogenicity_percentile``). Any number and
+  combination of these five criteria may be specified.
+- Not all prediction algorithms supported by pVACtools may support a
+  percentile rank. In order to alleviate this issue, and to provide percentile
+  ranks that have been consistently calculated, we have run predictions for
+  all class I algorithms supported by pVACtools on 100,000 reference peptides each in
+  lengths 8-11 and for the most common 1,000 human class I MHC alleles. These
+  predictions support a new feature in pVACtools: normalized percentiles
+  (``--use-normalized-percentiles``). With this option enabled, any of the
+  pVACtools pipelines will calculate normalized percentiles scores for all
+  predicted neoantigen candidates and selected prediction algorithms. These
+  normalized percentile ranks will be used in place of percentile ranks
+  calculated by the algorithms natively. Predictions for allele or lengths we
+  have not calculated reference scores will result in ``NA`` percentile ranks.
+  Turning on this option in class II runs or with non-human data will be
+  ignored. The peptides used in our predictions and the raw scores we calculated are
+  available at https://github.com/griffithlab/pvactools_percentiles_data.
+- In pVACbind and pVACfuse the ``Mutation`` column name in the various report
+  files has been renamed to ``Index`` in order to ensure consistency between
+  these and other tools.