lixiangchun Goto Github PK

aiplus

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

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.

comet

CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer

core-ml-sample

A Demo using Vision Framework building on Core ML Framework

decipherexpressionsignatures

Deciphering gene expression signature for high throughput data

deciphermutationalsignatures

Deciphering mutational signatures with alternative algorithms

deep-semi-nmf

Theano-based implementation of Deep Semi-NMF.

emu

An Expectation-Maximization algorithm to infer mutational signatures

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.

ggally

R package that extends ggplot2

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.

iseeek

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

lixiangchun.github.io

lxctk

My personal toolkit

maftools

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

mcp05

Scripts associated with Mouse ENCODE companion paper, Pope et al. Nature 2014 "Topologically-associating domains are stable units of replication-timing regulation" (doi:10.1038/nature13986)

minialign

fast and accurate alignment tool for PacBio and Nanopore long reads

miscell

Mining Information from Single-Cell high-throughput transcriptome data

miscellaneous-r-code

Code that might be useful to others for learning/demonstration purposes.

msig

mutation signature extraction

multi-dendrix

mutation_signature

mutationalprofiles

mymisccode