Pinned Repositories
ancestry_pipeline
Provides helper scripts for inferring local ancestry, performing ancestry-specific PCA, etc
atom
The hackable text editor
awesome-single-cell
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
BD2K-Summer-Workshop
Teaching the fundamentals of bioinformatics and data science. BD2K Summer Workshop 2016
Bios8366
Advanced Statistical Computing at Vanderbilt University's Department of Biostatistics
BME205_HW4
This is the description file for Kevin Karplus' BME205 class
dockerfiles
hydra
jpfeil's Repositories
jpfeil/hydra
jpfeil/awesome-single-cell
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
jpfeil/Bios8366
Advanced Statistical Computing at Vanderbilt University's Department of Biostatistics
jpfeil/bnpy
Bayesian nonparametric machine learning for Python
jpfeil/cmdstan
jpfeil/deuflix
jpfeil/dilated-attention-pytorch
(Unofficial) Implementation of dilated attention from "LongNet: Scaling Transformers to 1,000,000,000 Tokens" (https://arxiv.org/abs/2307.02486)
jpfeil/dockernator
This project contains my Dockerfiles for the tool used in the pimmuno project
jpfeil/DP_GP_cluster
jpfeil/fusion-1
jpfeil/gpu-docker
jpfeil/hydra-paper
jpfeil/ib_insync
Python sync/async framework for Interactive Brokers API
jpfeil/image-analysis
jpfeil/magvit2-pytorch
Implementation of MagViT2 Tokenizer in Pytorch
jpfeil/MoVQGAN
MoVQGAN - model for the image encoding and reconstruction
jpfeil/pyrwrapper
jpfeil/qsmooth
Smooth quantile normalization (qsmooth) is a generalization of quantile normalization, which is an average of the two types of assumptions about the data generation process: quantile normalization and quantile normalization between groups.
jpfeil/rnaseq-recompute-analysis
Analysis of RNA-seq recompute expression data
jpfeil/rstudio-docker
jpfeil/strander
jpfeil/taux-manuscript
tauX manuscript code
jpfeil/toil_docker_wrappers
jpfeil/toolbox
random scripts
jpfeil/torchscale
Foundation Architecture for (M)LLMs
jpfeil/Transgene
This is a repository to host the transgene tool. Transgene takes a snpeffed vcf and a peptide fasta , and returns 3 peptide fastas containing 9-, 10- and 15-mers harboring the called mutations
jpfeil/typhon
jpfeil/varscan2
Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
jpfeil/wambam
jpfeil/Workshop-2018