39 projects
varcode
Variant annotation in Python
pirlygenes
Curated cancer gene sets and reference expression data. Analysis lives in `trufflepig`.
vaxrank
Mutant peptide ranking for personalized cancer vaccines
topiary
Predict, filter, and rank MHC-presented peptides from any antigen source
isovar
Determine mutant protein sequences from RNA using assembly around variants
tcrsift
T-cell receptor selection for TCR-T studies from antigen specific culture and scRNA/VDJ sequencing
pirl-trufflepig
RNA tumor analysis driven by pirlygenes gene sets. Migrates the pirlygenes analyze pipeline into composable sub-commands with serializable intermediate state for incremental website-style runs.
gtfparse
Parsing library for extracting data frames of genomic features from GTF files
hitlist
Curated mass spectrometry evidence for MHC ligand data from IEDB and CEDAR
pyensembl
Python interface to Ensembl reference genome metadata
tsarina
Personalized cancer immunotherapy target selection from curated shared antigen data
mhctools
Python interface to MHC binding, presentation, immunogenicity, and antigen processing predictors
runplz
Tiny Modal-shaped job harness — one declaration, multiple backends (local Docker / Brev / Modal)
serializable
Base class with serialization helpers for user-defined Python objects
mhcseqs
MHC sequence curation and binding groove extraction
mhcgnomes
Python library for parsing MHC nomenclature in the wild
pepdata
Immunological peptide datasets and amino acid properties
golfy
Heuristic peptide pool optimization for ELISpot and other immunological assays
weirdo
Metrics of immunological foreignness for candidate T-cell epitopes
datacache
Helpers for transparently downloading datasets
sercol
Rich collection class with grouping and filtering helpers
fancyimpute
Matrix completion and feature imputation algorithms
parakeet
Runtime compiler for numerical Python.
msmhc
Looking for dark matter of the MHC ligandome in mass spectra
mutexp
Predict mutation-specific expression from DNA features
scalarmix
Scalar bimodal Gaussian mixture models
openvax_project_template
Project template for OpenVax Python projects
mhcnames
Python library for MHC nomenclature parsing
typechecks
Helper functions for runtime type checking
pepnet
Neural networks for amino acid sequences
knnimpute
k-Nearest Neighbor imputation
tinytimer
Tiny Python benchmarking library
censored_regression
Linear regression where some of the labels are lower bounds
epitopes
Python interface to IEDB and other immune epitope data
dsltools
Helpers for creating and traversing recursively nested data structures in Python.
TreeLike
Helpers for creating and traversing recursively nested data structures in Python.
shiver
A multi-threaded work queue for functions compiled with llvmpy
loopjit
Syntax, types, and codegen helpers for compiling loop-oriented numerical code to LLVM in Python.
moving_pictures
Create a movie from a sequence of images in Python (uses PIL and ffmpeg)
