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academicpages.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

algorithms

Minimal examples of data structures and algorithms in Python

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

episcanpy

Episcanpy: Epigenomics Single Cell Analysis in Python

gillespie

Python implementation of Gillespie's algorithm

interpretableautoencoders

late

Imputation of single cell RNA-sequencing data with autoencoder

magic

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

mean-noise-fitness-landscapes

Scripts to reproduce analysis of Schmiedel et al. "Empirical noise-mean fitness landscapes and the evolution of gene expression" bioRxiv, 2018

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

phate

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

prmlt

Matlab code for machine learning algorithms in book PRML

python

All Algorithms implemented in Python

saucie

scanpy

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

scgen

Single cell perturbation prediction

scnmt-seq

single-cell Nucleosome Methylation Transcription

scnmt_gastrulation

scNMT-seq gastrulation

scnn

Deep learning methods for the analysis of single-cell data

scprep

A collection of scripts and tools for loading, processing, and handling single cell data.

scvi

Deep generative modeling for single-cell transcriptomics

stream

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

tensorflow-autoencoders

Implementations of autoencoder, generative adversarial networks, variational autoencoder and adversarial variational autoencoder

tensorflow-examples

TensorFlow Tutorial and Examples for Beginners (support TF v1 & v2)

tybalt

Training and evaluating a variational autoencoder for pan-cancer gene expression data

vae_protein_function

Protein function prediction using a variational autoencoder

variational-autoencoder

Variational autoencoder implementation using Tensorflow and Python

variational-autoencoder-1

Variational autoencoder implemented in tensorflow and pytorch (including inverse autoregressive flow)

vasc

Variational autoencoder for single cell RNA-seq datasets

vde

Variational Autoencoder for Dimensionality Reduction of Time-Series