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Implement new select, select_class_i, and select_class_ii algorithm options to run subset of algorithms #1452

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Implement new select, select_class_i, and select_class_ii algorithm o…
susannasiebert Aug 12, 2026
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Add column to algorithm table to indicate whether it is included in t…
susannasiebert Aug 13, 2026
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Update docs/pvacbind/features.rst
susannasiebert Aug 31, 2026
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33 changes: 30 additions & 3 deletions docs/pvacbind/features.rst
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Expand Up @@ -46,7 +46,11 @@ and immunogenicity algorithms.
By using the IEDB RESTful web interface, pVACbind leverages their extensive support of different prediction algorithms.

In addition to IEDB-supported prediction algorithms, we've also added support
for a variety of additional algorithms.
for a variety of additional algorithms. The following table lists all algorithms supported
by pVACbind, whether the algorithm is a MHC class I or class II algorithm, what type of scoring
the algorithm returns (binding, presentation, or immunogenicity), whether it supports
percentile ranks natively, supports normalized percentile ranks (``--use-normalized-percentiles``
flag), and whether the ``select`` algorithm shortcut includes this algorithm.
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.. list-table::
:header-rows: 1
Expand All @@ -57,138 +61,161 @@ for a variety of additional algorithms.
- Prediction Type
- Supports Percentile Ranks?
- Supports Normalized Percentile Ranks?
- Included On "select" Strategy?
* - BigMHC_EL
-
- MHC Class I
- Presentation
- no
- yes
- yes
* - BigMHC_IM
-
- MHC Class I
- Immunogenicity
- no
- yes
- yes
* - DeepImmuno
-
- MHC Class I
- Immunogenicity
- no
- yes
* - ImmuoScope_IM
- yes
* - ImmuScope_IM
-
- MHC Class II
- Immunogenicity
- no
- no
- yes
* - MHCflurry
-
- MHC Class I
- Binding
- yes
- yes
- yes
* - MHCflurryEL
-
- MHC Class I
- Presentation, Processing
- yes (Presentation only)
- yes (Presentation and Processing)
- yes (Presentation and Processing)
* - MHCnuggetsI
-
- MHC Class I
- Binding
- yes
- yes
- no
* - MHCnuggetsII
-
- MHC Class II
- Binding
- yes
- no
- yes
* - MixMHC2pred
-
- MHC Class II
- Presentation
- yes
- no
- yes
* - MixMHCpred
-
- MHC Class I
- Binding
- yes
- yes
- yes
* - NNalign
- 2.3
- MHC Class II
- Binding
- yes
- no
- no
* - NetMHC
- 4.0
- MHC Class I
- Binding
- yes
- yes
- no
* - NetMHCIIpan
- 4.0 (not supported by standalone IEDB), 4.1 (default), 4.2., 4.3
- MHC Class II
- Binding
- yes
- no
- yes
* - NetMHCIIpanEL
- 4.0 (not supported by standalone IEDB), 4.1 (default), 4.2., 4.3
- MHC Class II
- Presentation
- yes
- no
- yes
* - NetMHCcons
- 1.1
- MHC Class I
- Binding
- yes
- yes
- no
* - NetMHCpan
- 4.1
- MHC Class I
- Binding
- yes
- yes
- yes
* - NetMHCpanEL
- 4.1
- MHC Class I
- Presentation
- yes
- yes
- yes
* - PRIME
-
- MHC Class I
- Immunogenicity
- yes
- yes
* - Pickpocket
- yes
* - PickPocket
- 1.1
- MHC Class I
- Binding
- yes
- yes
- yes
* - SMM
- 1.0
- MHC Class I
- Binding
- yes
- yes
- no
* - SMMPMBEC
- 1.0
- MHC Class I
- Binding
- yes
- yes
- yes
* - SMMalign
- 1.1
- MHC Class II
- Binding
- yes
- no
- yes

**Calculation of normalized percentiles**

Expand Down
33 changes: 30 additions & 3 deletions docs/pvacfuse/features.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,11 @@ and immunogenicity algorithms.
By using the IEDB RESTful web interface, pVACfuse leverages their extensive support of different prediction algorithms.

In addition to IEDB-supported prediction algorithms, we've also added support
for a variety of additional algorithms.
for a variety of additional algorithms. The following table lists all algorithms supported
by pVACfuse, whether the algorithm is a MHC class I or class II algorithm, what type of scoring
the algorithm returns (binding, presentation, or immunogenicity), whether it supports
percentile ranks natively, supports normalized percentile ranks (``--use-normalized-percentiles``
flag), and whether the ``select`` algorithm shortcut includes this algorithm.

.. list-table::
:header-rows: 1
Expand All @@ -57,138 +61,161 @@ for a variety of additional algorithms.
- Prediction Type
- Supports Percentile Ranks?
- Supports Normalized Percentile Ranks?
- Included On "select" Strategy?
* - BigMHC_EL
-
- MHC Class I
- Presentation
- no
- yes
- yes
* - BigMHC_IM
-
- MHC Class I
- Immunogenicity
- no
- yes
- yes
* - DeepImmuno
-
- MHC Class I
- Immunogenicity
- no
- yes
* - ImmuoScope_IM
- yes
* - ImmuScope_IM
-
- MHC Class II
- Immunogenicity
- no
- no
- yes
* - MHCflurry
-
- MHC Class I
- Binding
- yes
- yes
- yes
* - MHCflurryEL
-
- MHC Class I
- Presentation, Processing
- yes (Presentation only)
- yes (Presentation and Processing)
- yes (Presentation and Processing)
* - MHCnuggetsI
-
- MHC Class I
- Binding
- yes
- yes
- no
* - MHCnuggetsII
-
- MHC Class II
- Binding
- yes
- no
- yes
* - MixMHC2pred
-
- MHC Class II
- Presentation
- yes
- no
- yes
* - MixMHCpred
-
- MHC Class I
- Binding
- yes
- yes
- yes
* - NNalign
- 2.3
- MHC Class II
- Binding
- yes
- no
- no
* - NetMHC
- 4.0
- MHC Class I
- Binding
- yes
- yes
- no
* - NetMHCIIpan
- 4.0 (not supported by standalone IEDB), 4.1 (default), 4.2., 4.3
- MHC Class II
- Binding
- yes
- no
- yes
* - NetMHCIIpanEL
- 4.0 (not supported by standalone IEDB), 4.1 (default), 4.2., 4.3
- MHC Class II
- Presentation
- yes
- no
- yes
* - NetMHCcons
- 1.1
- MHC Class I
- Binding
- yes
- yes
- no
* - NetMHCpan
- 4.1
- MHC Class I
- Binding
- yes
- yes
- yes
* - NetMHCpanEL
- 4.1
- MHC Class I
- Presentation
- yes
- yes
- yes
* - PRIME
-
- MHC Class I
- Immunogenicity
- yes
- yes
* - Pickpocket
- yes
* - PickPocket
- 1.1
- MHC Class I
- Binding
- yes
- yes
- yes
* - SMM
- 1.0
- MHC Class I
- Binding
- yes
- yes
- no
* - SMMPMBEC
- 1.0
- MHC Class I
- Binding
- yes
- yes
- yes
* - SMMalign
- 1.1
- MHC Class II
- Binding
- yes
- no
- yes

**Calculation of normalized percentiles**

Expand Down
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