lixiangchun

mynotebook

My daily notebook on bioinformatic data analysis and machine learning

decipherMutationalSignatures

Deciphering mutational signatures with alternative algorithms

iSEEEK

A universal approach for integrating super large-scale single-cell transcriptomes by exploring gene rankings

Miscell

Mining Information from Single-Cell high-throughput transcriptome data

AIplus

AI + medical imaging, cancer genomics, and single cell etc

lxctk

My personal toolkit

tGPT

Generative pretraining on rankings of top-expressing genes

survminer

Survival Analysis and Visualization

ascat

ASCAT copy number R package

awesome-deepbio

A curated list of awesome deep learning applications in the field of computational biology

brms

Fit Bayesian generalized (non-)linear multilevel models using Stan for full Bayesian inference.

Core-ML-Sample

A Demo using Vision Framework building on Core ML Framework

fermi-lite

Standalone C library for assembling Illumina short reads in small regions

forestmodel

generative-models

Collection of generative models, e.g. GAN, VAE in Tensorflow, Keras, and Pytorch.

GenVisR

Genome data visualizations

GenVisR-1

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/GenVisR.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=GenVisR.

HMMcopy

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/HMMcopy.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=HMMcopy.

lixiangchun.github.io

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

minialign

fast and accurate alignment tool for PacBio and Nanopore long reads

openslide-python

Python bindings to OpenSlide

psofs

Particle swarm optimization for feature selection

rstan

RStan, the R interface to Stan

Rtsne

R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding

shinystan

shinystan R package

SomaticSignatures

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/SomaticSignatures.html Contributions: http://bioconductor.org/packages/release/bioc/html/SomaticSignatures.html, https://github.com/julian-gehring/SomaticSignatures-release. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=SomaticSignatures.

stan

Stan development repository (home page is linked below). The master branch contains the current release. The develop branch contains the latest stable development. See the Developer Process Wiki for details.

tensorlayer

TensorLayer: Deep Learning and Reinforcement Learning Library for TensorFlow.

WIT

WSI Inspection via Transformer