neoepiscope - neoepiscope v0.7.0

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

- Python
Published by nellore almost 4 years ago

neoepiscope - 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

- Python
Published by maryawood over 5 years ago

neoepiscope - neoepiscope v0.4.1

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

- Python
Published by maryawood almost 6 years ago

neoepiscope - 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

- Python
Published by maryawood almost 6 years ago

neoepiscope - neoepiscope v0.3.9

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

- Python
Published by maryawood about 6 years ago

neoepiscope - neoepiscope v0.3.8

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

- Python
Published by maryawood over 6 years ago

neoepiscope - neoepiscope v0.3.7

• Fixes bug in VCF processing to identify VAF field

- Python
Published by maryawood over 6 years ago

neoepiscope - 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)

- Python
Published by maryawood almost 7 years ago

neoepiscope - neoepiscope v0.3.5

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

- Python
Published by maryawood about 7 years ago

neoepiscope - neoepiscope v0.3.3

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

- Python
Published by maryawood over 7 years ago

neoepiscope - neoepiscope v0.3.2

• Adds processing step to break down haplotypes containing incompatible variants that are reported to be phased together

- Python
Published by maryawood over 7 years ago

neoepiscope - neoepiscope v0.3.0

• Corrects previous variant phasing error by including homozygous variants in relevant haplotype blocks
• Corrects handling of intron-exon boundary deletions to truncate transcripts
• Corrects annotation of transcripts with start/stop codons split across multiple exons
• Expands functionality to allow for variant phasing using either HapCUT2 or GATK's ReadBackedPhasing
• Updates default gene annotation for hg38 to GENCODE v29
• Updates code for compatibility with intervaltree v3.0.2

- Python
Published by maryawood over 7 years ago

neoepiscope - neoepiscope v0.2.1

• Adjusts neoepiscope prep functionality to accept VCFs only for users who do not wish to run haplotype phasing

• Updates neoepiscope download functionality for python3 compatibility

• Includes bug fixes for edge cases in handing indel mutations, accommodating "N"/"<DEL>" variants from Pindel VCFs

- Python
Published by maryawood over 7 years ago

neoepiscope - neoepiscope v0.2.0

First public release of software that predicts neoepitopes from tumor/normal DNA-seq data.

- Python
Published by nellore almost 8 years ago