iskandr

knnimpute

Python implementations of kNN imputation

adversarial-impute

Possibly ill-fated experimented with Generative Adversarial Imputation

censored_regression

Linear regression with lower-bound labels

brainmets

Survival prediction for brain metastases

bytestar

Analyze Python bytecode using an SSA control flow graph representation

mhcpred

MHC Binding Prediction

nnseq

Multi-sequence learning using recurrent neural networks

immunesearch

Search for peptide substrings in IEDB T-cell assay data

keras

Theano-based Deep Learning library (convnets, recurrent neural networks, and more).

pca-magic

PCA that iteratively replaces missing data

prototype-pan-allele-class2

Prototype of a pan-allele Class II MHC binding predictor

avroglob

Bundle together the contents of a directory into a single AVRO file

bioseq

Compact library for working with biological sequences (DNA, RNA, and Proteins)

cohort-seq2hla

Run the TRON seq2HLA script on a collection of related RNA samples

CompleteThat

CompleteThat is a python package that solves the low rank matrix completion problem. Given a low rank matrix with partial entries the package solves an optimization problem to estimate the missing entries.

fermikit

De novo assembly based variant calling pipeline for Illumina short reads

hadoop-variant-caller

Simple repo containing a Hadoop MapReduce configured via Maven

insert-aligner

k-mer aligner to detect where a transposon was inserted in a longer sequence

iskandr.github.io

keras-GAN

Generative Adversarial Networks with Keras

mhc_ligandome

MHC binding predictions for human proteome

mhcseqs

Sequence of MHCs across species

mr-python-variant-caller

Simple somatic variant caller in Python w/ Hadoop Streaming

mri_biopsy

Predict presence of prostate cancer from pre-biopsy MRI images

pepsearch

Search reference proteomes for short peptides

sam-perf-experiments

Simple performance test of SAM parsing performance in Python

scikit-bio

scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.

scikit-learn

scikit-learn: machine learning in Python

tinytimer

Tiny benchmarking library for Python

vaxrank-application-note-2017

Draft of a Bioinformatics Application Note for Vaxrank