<img src="docs/figures/neofox_logo_small.png" width="10%"> NeoFox - NEOantigen Feature tOolboX

NeoFox annotates neoantigen candidate sequences with published neoantigen features.

For a detailed documentation, please check out https://neofox.readthedocs.io

If you use NeoFox, please cite the following publication:
Franziska Lang, Pablo Riesgo-Ferreiro, Martin Löwer, Ugur Sahin, Barbara Schrörs, NeoFox: annotating neoantigen candidates with neoantigen features, Bioinformatics, Volume 37, Issue 22, 15 November 2021, Pages 4246–4247, https://doi.org/10.1093/bioinformatics/btab344

Table of Contents

1 Implemented neoantigen features
2 NeoFox requirements
3 Usage from the command line
4 Input data
5 Output data

1 Implemented Neoantigen Features

NeoFox covers the following neoantigen features and prediction algorithms:

| Name | Reference | DOI | |---------------------------------------------------------|--------------------------------------------------------------------------|-------------------------------------------------------------------------------------------| | MHC I binding affinity/rank score (netMHCpan-v4.1) | Reynisson et al, 2020, Nucleic Acids Research | https://doi.org/10.4049/jimmunol.1700893 | | MHC II binding affinity/rank score (netMHCIIpan-v4.3) | Nilsson et al, 2023, Science Adv. | https://doi.org/10.1126/sciadv.adj6367 | | MixMHCpred score v2.2 § | Bassani-Sternberg et al., 2017, PLoS Comp Bio; Gfeller, 2018, J Immunol. | https://doi.org/10.1371/journal.pcbi.1005725 , https://doi.org/10.4049/jimmunol.1800914 | | MixMHC2pred score v2.0.2 § | Racle et al, 2019, Nat. Biotech. 2019 | https://doi.org/10.1038/s41587-019-0289-6 | | Differential Agretopicity Index (DAI) | Duan et al, 2014, JEM; Ghorani et al., 2018, Ann Oncol. | https://doi.org/10.1084/jem.20141308 | | Self-Similarity | Bjerregaard et al, 2017, Front Immunol. | https://doi.org/10.3389/fimmu.2017.01566 | | IEDB immunogenicity | Calis et al, 2013, PLoS Comput Biol. | https://doi.org/10.1371/journal.pcbi.1003266 | | Neoantigen dissimilarity | Richman et al, 2019, Cell Systems | https://doi.org/10.1016/j.cels.2019.08.009 | | PHBR-I § | Marty et al, 2017, Cell | https://doi.org/10.1016/j.cell.2017.09.050 | | PHBR-II § | Marty Pyke et al, 2018, Cell | https://doi.org/10.1016/j.cell.2018.08.048 | | Generator rate | Rech et al, 2018, Cancer Immunology Research | https://doi.org/10.1158/2326-6066.CIR-17-0559 | | Recognition potential § | Łuksza et al, 2017, Nature; Balachandran et al, 2017, Nature | https://doi.org/10.1038/nature24473 , https://doi.org/10.1038/nature24462 | | Vaxrank | Rubinsteyn, 2017, Front Immunol | https://doi.org/10.3389/fimmu.2017.01807 | | Priority score | Bjerregaard et al, 2017, Cancer Immunol Immunother. | https://doi.org/10.1007/s00262-017-2001-3 | | PRIME § | Schmidt et al., 2021, Cell Reports Medicine | https://doi.org/10.1016/j.xcrm.2021.100194 | | HEX § | Chiaro et al., 2021, Cancer Immunology Research | https://doi.org/10.1158/2326-6066.CIR-20-0814 |

§ currently not supported for mouse

2 NeoFox Requirements

NeoFox depends on the following tools:

• Python 3.11
• BLAST 2.10.1
• netMHCpan 4.1
• netMHCIIpan 4.3
• MixMHCpred 2.2 (optional)
• MixMHC2pred 2.0.2 (optional)
• PRIME 2.0 (optional)

Install from PyPI:

pip install neofox

Or install from bioconda:

conda install bioconda::neofox

3 Usage from the command line

NeoFox can be used from the command line as shown below or programmatically (see https://neofox.readthedocs.io for more information).

neofox --input-file neoantigens_candidates.tsv \
    --patient-data patient_data.txt \
    --output-folder /path/to/out \
    [--output-prefix out_prefix]  \
    [--organism human|mouse]  \
    [--rank-mhci-threshold 2.0] \
    [--rank-mhcii-threshold 5.0] \
    [--num-cpus] \
    [--config] \
    [--patient-id] \
    [--with-all-neoepitopes] \
    [--verbose]

• --input-file: tab-separated values table with neoantigen candidates represented by long mutated peptide sequences as described here (extensions .txt and .tsv) or JSON file neoantigens in NeoFox model format as described here (extension .json)
• --patient-data: a table of tab separated values containing metadata on the patient as described here
• --output-folder: path to the folder to which the output files should be written
• --output-prefix: prefix for the output files (optional)
• --with-all-neoepitopes: output annotations for all MHC-I and MHC-II neoepitopes on all HLA alleles (optional)
• --rank-mhci-threshold: MHC-I epitopes with a netMHCpan predicted rank greater than or equal than this threshold will be filtered out (optional)
• --rank-mhcii-threshold: MHC-II epitopes with a netMHCIIpan predicted rank greater than or equal than this threshold will be filtered out (optional)
• --organism: the organism to which the data corresponds. Possible values: [human, mouse]. Default value: human
• --num-cpus: number of CPUs to use (optional)
• --config: a config file with the paths to dependencies as shown below (optional)
• --patient-id: patient identifier (optional, this is only relevant if the column patientIdentifier is missing in the candidate input file)
• --verbose: get detailed logs

The optional config file with the paths to the dependencies can look like this:

NEOFOX_REFERENCE_FOLDER=path/to/reference/folder
NEOFOX_BLASTP=path/to/ncbi-blast-2.10.1+/bin/blastp
NEOFOX_NETMHCPAN=path/to/netMHCpan-4.1/netMHCpan
NEOFOX_NETMHC2PAN=path/to/netMHCIIpan-4.3/netMHCIIpan
NEOFOX_MIXMHCPRED=path/to/MixMHCpred-2.2/MixMHCpred
NEOFOX_MIXMHC2PRED=path/to/MixMHC2pred-2.0.1/MixMHC2pred_unix
NEOFOX_MAKEBLASTDB=path/to/ncbi-blast-2.8.1+/bin/makeblastdb
NEOFOX_PRIME=/path/to/PRIME-2.0/PRIME

4 Input data

4.1 Neoantigen candidates in tabular format

This is an dummy example of a table with neoantigen candidates:

| gene | wildTypeXmer | mutatedXmer | patientIdentifier | rnaExpression | rnaVariantAlleleFrequency | dnaVariantAlleleFrequency | external_annotation_1 | external_annotation_2 | |-------|-----------------------------|-----------------------------|-------------------|---------------|---------------------------|---------------------------|-----------------------|-----------------------| | BRCA2 | AAAAAAAAAAAAALAAAAAAAAAAAAA | AAAAAAAAAAAAAFAAAAAAAAAAAAA | Ptx | 7.942 | 0.85 | 0.34 | some_value | some_value | | BRCA2 | AAAAAAAAAAAAAMAAAAAAAAAAAAA | AAAAAAAAAAAAARAAAAAAAAAAAAA | Ptx | 7.942 | 0.85 | 0.34 | some_value | some_value | | BRCA2 | AAAAAAAAAAAAAGAAAAAAAAAAAAA | AAAAAAAAAAAAAKAAAAAAAAAAAAA | Ptx | 7.942 | 0.85 | 0.34 | some_value | some_value | | BRCA2 | AAAAAAAAAAAAACAAAAAAAAAAAAA | AAAAAAAAAAAAAEAAAAAAAAAAAAA | Ptx | 7.942 | 0.85 | 0.34 | some_value | some_value | | BRCA2 | AAAAAAAAAAAAAKAAAAAAAAAAAAA | AAAAAAAAAAAAACAAAAAAAAAAAAA | Ptx | 7.942 | 0.85