jerome-f
Statistical Geneticist, Computational Biologist and AI/ML scientist.
Genentech Inc.San Francisco
Pinned Repositories
apricot
apricot implements submodular optimization for the purpose of selecting subsets of massive data sets to train machine learning models quickly. See the documentation page: https://apricot-select.readthedocs.io/en/latest/index.html
basenji
Sequential regulatory activity predictions with deep convolutional neural networks.
bolt
10x faster matrix and vector operations
CADD-scripts
CADD scripts release for offline scoring. For more information about CADD, please visit our website
ccc
coloc
Repo for the R package coloc
coloc_scripts
conformal-prediction
Lightweight, useful implementation of conformal prediction on real data.
CSC509
For the CSC509 SFSU Course Deep Learning in Medical Imaging
dgn2vec
Pathogenic gene prediction based on network embedding
jerome-f's Repositories
jerome-f/CADD-scripts
CADD scripts release for offline scoring. For more information about CADD, please visit our website
jerome-f/coloc
Repo for the R package coloc
jerome-f/coloc_scripts
jerome-f/conformal-prediction
Lightweight, useful implementation of conformal prediction on real data.
jerome-f/dyvider
Dynamic programming algorithms for exact linear clustering in networks.
jerome-f/enformer-pytorch
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
jerome-f/echtvar
using all the bits for echt rapid variant annotation and filtering
jerome-f/flinty
A Simple and Flexible Test of Sample Exchangeability with Applications to Statistical Genomics
jerome-f/GBC
GBC (short for GenoType Blocking Compressor) is a blocking compressor for genotype data, which aims at creating a unified and flexible structure-GenoType Block (GTB) for genotype data in the variant call format (VCF) files.
jerome-f/GeneBayes
jerome-f/gget
š§¬ gget enables efficient querying of genomic reference databases
jerome-f/gwaslab
A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/ https://gwaslab.com/python-gwaslab/
jerome-f/GWLD
jerome-f/hail
Scalable genomic data analysis.
jerome-f/LAVA2
jerome-f/ngboost
Natural Gradient Boosting for Probabilistic Prediction
jerome-f/NoiseCut
jerome-f/PheWAS
The PheWAS R package
jerome-f/PrCaFineMapping
jerome-f/pyblip
Bayesian Linear Programming for Resolution-Adaptive Signal Detection
jerome-f/regenie
regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
jerome-f/regenie-bioconda-recipe
jerome-f/rlvi
Robust Learning using Variational Inference
jerome-f/slalom
SLALOM (suspicious loci analysis of meta-analysis summary statistics)
jerome-f/susieR
R package for "sum of single effects" regression.
jerome-f/tabular-benchmark
jerome-f/ukbb_common
jerome-f/ukbb_pan_ancestry
Analyses conducting GWAS across the UKBB diverse superpopulations
jerome-f/xgboost-mod
Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Dask, Flink and DataFlow
jerome-f/zlib-m
A massively spiffy yet delicately unobtrusive compression library.