neoepiscope v0.7.0

• Predicts neopeptides from A-to-I edits in REDIportal database with --rna-edits

neoepiscope v0.5.0

Updates translation algorithm for increased accuracy

• Compatible with annotated stop codon readthrough (retains X as unknown amino acid)
• Compatible with selenocysteine transcripts (retains X and flags as possible selenocysteine)
• Supports annotated start codons of noncanonical sequence

Updates GRCh38 annotations to GENCODE v35

neoepiscope v0.4.1

• Eliminates python 2 compatibility
• Updates binding affinity predictions for MHCflurry v2 compatibility

neoepiscope v0.4.0

• Adds functionality for reporting mutation-level expression
• Adds functionality for reporting/filtering on transcript-level expression
• Adds functionality for the mm10 genome build
• Adds functionality for NetMHCpan v4.1 and NetMHCIIpan v4.0
• Fixes bug in mhcnuggets binding predictions

neoepiscope v0.3.9

• Updates MHC allele processing for binding predictions
• Changes warning to note in neoepiscope swap
• Updates run instructions in README

neoepiscope v0.3.8

• Adds support for mouse genome build mm9
• Fixes bug in running with user-supplied genome builds

neoepiscope v0.3.7

• Fixes bug in VCF processing to identify VAF field

neoepiscope v0.3.6

• Adds functionality for a variety of new binding affinity prediction tools
• Adds transcript type, gene ID, gene name, and IEDB epitope identifier fields to output
• Removes necessity for neoepiscope swap mode (functionality retained)

neoepiscope v0.3.5

• Updates haplotype processing to fix bug with complex indels
• Adds MANIFEST.in to address bug in PyPI installation

neoepiscope v0.3.3

• Fixes bug that prevented processing of user-specified reference data for use in neoepitope predictions