jacobkimmel Goto Github PK

agingnets

regulatory network analysis of aging related genetic variants

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

deepcell

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

deepmask

Torch implementation of DeepMask and SharpMask

deprior

dnachisel

:pencil2: A versatile DNA sequence optimizer

eleven

qPCR analysis tools for Python

examples

A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.

fcdensenet_pytorch

PyTorch implementation of Fully Convolutional DenseNets for Semantic Segmentation

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

keras

Deep Learning library for Python. Runs on TensorFlow, Theano, or CNTK.

lanternfish

Deep convolutional neural networks for biological motion analysis

microarray_parser

parses data from an affymetrix microarray to remove noise between samples prior to ontology analsysis

musc_tracker

Bipartite tracker for muscle stem cells

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"

ps_decomp

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

pyfitdecay

Two Python implementations of sum of exponentials fitting to data

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

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