jacobkimmel
Head of Research, @NewLimit | previously Principal Investigator @calico, PhD @UCSF | Interested in aging, genomics, machine learning
@newlimitsan francisco, ca
Pinned Repositories
scnym
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
velodyn
Dynamical systems methods for RNA velocity analysis
heteromotility
Quantitative analysis of cell motility behaviors
fcdensenet_pytorch
PyTorch implementation of Fully Convolutional DenseNets for Semantic Segmentation
lanternfish
Deep convolutional neural networks for biological motion analysis
ps_decomp
Periodic plus smooth image decomposition, as described by Moisan (http://www.math-info.univ-paris5.fr/~moisan/papers/2009-11r.pdf)
pytorch_convgru
Convolutional Gated Recurrent Units implemented in PyTorch
pytorch_modelsize
Estimates the size of a PyTorch model in memory
pytorch_modelsummary
Summarizes PyTorch models
jacobkimmel's Repositories
jacobkimmel/pytorch_modelsize
Estimates the size of a PyTorch model in memory
jacobkimmel/pytorch_convgru
Convolutional Gated Recurrent Units implemented in PyTorch
jacobkimmel/ps_decomp
Periodic plus smooth image decomposition, as described by Moisan (http://www.math-info.univ-paris5.fr/~moisan/papers/2009-11r.pdf)
jacobkimmel/lanternfish
Deep convolutional neural networks for biological motion analysis
jacobkimmel/fcdensenet_pytorch
PyTorch implementation of Fully Convolutional DenseNets for Semantic Segmentation
jacobkimmel/DeepCell
@jkimmel's fork of DeepCell, implementing multiprocessing support and a big refactor for clarity
jacobkimmel/musc_tracker
Bipartite tracker for muscle stem cells
jacobkimmel/anchor
:anchor: Find bimodal, unimodal, and multimodal features in your data
jacobkimmel/anndata
Annotated data.
jacobkimmel/CellBender
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
jacobkimmel/coolname
Random Name and Slug Generator
jacobkimmel/DEprior
jacobkimmel/DnaChisel
:pencil2: A versatile DNA sequence optimizer
jacobkimmel/GSEA.py
Python implementation of Gene Set Enrichment Analysis (GSEA) method
jacobkimmel/GSEApy
Gene Set Enrichment Analysis in Python
jacobkimmel/hmR
Heteromotility Data Analysis in R
jacobkimmel/jacobkimmel.github.io
personal website
jacobkimmel/kb_python
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
jacobkimmel/myodyn
Single cell behavioral and transcriptomic of aging muscle stem cells
jacobkimmel/non-parametric-transformers
Code for "Self-Attention Between Datapoints: Going Beyond Individual Input-Output Pairs in Deep Learning"
jacobkimmel/sc_progress
Plotting the progress of single cell genomics
jacobkimmel/scanpy
Single-Cell Analysis in Python. Scales to >1M cells.
jacobkimmel/scg_lib_structs
Collections of library structure and sequence of popular single cell genomic methods
jacobkimmel/scVI
Deep generative modeling for single-cell transcriptomics
jacobkimmel/scvi-tutorials
Notebooks used in scvi-tools tutorials
jacobkimmel/set_transformer
Pytorch implementation of set transformer
jacobkimmel/seurat
R toolkit for single cell genomics
jacobkimmel/supermariopy
python library, scripts and notebooks that are usfull from time to time
jacobkimmel/tools
Things we use regularly
jacobkimmel/velocyto.py
RNA velocity estimation in Python