Xinhui Liao's repositories
Accucopy
Accucopy is a computational method that infers Allele-specific Copy Number alterations from low-coverage low-purity tumor sequencing Data.
Accurity
Accurity is a computational method that infers tumor purity and tumor cell ploidy from tumor-normal WGS (whole exome will probably work too) data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs).
bamgineer
Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
cnv_facets
Somatic copy variant caller (CNV) for next generation sequencing
conv_arithmetic
A technical report on convolution arithmetic in the context of deep learning
ctat-genome-lib-builder
Software used by Trinity CTAT for building CTAT Genome Libs, resource databases shared by Trinity CTAT components
DeepLearning-500-questions
深度学习500问，以问答形式对常用的概率知识、线性代数、机器学习、深度学习、计算机视觉等热点问题进行阐述，以帮助自己及有需要的读者。 全书分为18个章节，50余万字。由于水平有限，书中不妥之处恳请广大读者批评指正。 未完待续............ 如有意合作，联系scutjy2015@163.com 版权所有，违权必究 Tan 2018.06
dl-visuals
Over 200 figures and diagrams of the most popular deep learning architectures and layers FREE TO USE in your blog posts, slides, presentations, or papers.
EasyFuse
EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
facets
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
forestploter
Draw forestplot in R
geomlime
ggplot geom_lime()
gerde.github.io
Gerde's blog
IMGTHLA
Github for files currently published in the IPD-IMGT/HLA FTP Directory hosted at the European Bioinformatics Institute
LinearFold
The new source code of the LinearFold, linear-time prediction for RNA secondary structures
MANTIS
Microsatellite Analysis for Normal-Tumor InStability
patchwork
The Composer of ggplots
prtpy
Number partitioning in Python
r-shiny-electron
WIP: Electron and R shiny
ref-gen
Human reference genome analysis sets
rentrez
talk with NCBI entrez using R
single-cell-best-practices
https://www.sc-best-practices.org
somaticseq
An ensemble approach to accurately detect somatic mutations using SomaticSeq
transformers
🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.
variantValidator
Public repository for VariantValidator project