Releases: pdxgx/neoepiscope
Releases · pdxgx/neoepiscope
neoepiscope v0.7.0
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 andNetMHCIIpan
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