jacobkimmel

pytorch_modelsize

Estimates the size of a PyTorch model in memory

pytorch_convgru

Convolutional Gated Recurrent Units implemented in PyTorch

ps_decomp

Periodic plus smooth image decomposition, as described by Moisan (http://www.math-info.univ-paris5.fr/~moisan/papers/2009-11r.pdf)

lanternfish

Deep convolutional neural networks for biological motion analysis

fcdensenet_pytorch

PyTorch implementation of Fully Convolutional DenseNets for Semantic Segmentation

DeepCell

@jkimmel's fork of DeepCell, implementing multiprocessing support and a big refactor for clarity

musc_tracker

Bipartite tracker for muscle stem cells

anchor

:anchor: Find bimodal, unimodal, and multimodal features in your data

anndata

Annotated data.

CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

coolname

Random Name and Slug Generator

DEprior

DnaChisel

:pencil2: A versatile DNA sequence optimizer

GSEA.py

Python implementation of Gene​ ​Set​ ​Enrichment​ ​Analysis​ (GSEA) method

GSEApy

Gene Set Enrichment Analysis in Python

hmR

Heteromotility Data Analysis in R

jacobkimmel.github.io

personal website

kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

myodyn

Single cell behavioral and transcriptomic of aging muscle stem cells

non-parametric-transformers

Code for "Self-Attention Between Datapoints: Going Beyond Individual Input-Output Pairs in Deep Learning"

sc_progress

Plotting the progress of single cell genomics

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scg_lib_structs

Collections of library structure and sequence of popular single cell genomic methods

scVI

Deep generative modeling for single-cell transcriptomics

scvi-tutorials

Notebooks used in scvi-tools tutorials

set_transformer

Pytorch implementation of set transformer

seurat

R toolkit for single cell genomics

supermariopy

python library, scripts and notebooks that are usfull from time to time

tools

Things we use regularly

velocyto.py

RNA velocity estimation in Python