WillJackson94

FIt-SNE

Fast Fourier Transform-accelerated Interpolation-based t-SNE (FIt-SNE)

netTCR

predicting peptide and TCR interaction

cellassign

Automated, probabilistic assignment of cell types in scRNA-seq data

CIBERSORT

A shell to facilitate loading / running CIBERSORT software in structured environments

seq2HLA

In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.

ggtree

:christmas_tree:Visualization and annotation of phylogenetic trees

cbioportal

cBioPortal for Cancer Genomics

manta

Structural variant and indel caller for mapped sequencing data

singleLiverCells

Scripts for processing single liver cells RNA-Seq 10X Genomics Data

HCA-reproducibility

A case study on the detailed reproducibility of a human cell atlas project

wot

A software package for analyzing snapshots of developmental processes

PyHLA

Python for HLA analysis: summary, association analysis, zygosity test and interaction test

bedtools2

bedtools - the swiss army knife for genome arithmetic

gatk4-somatic-snvs-indels

This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

xgboost

Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Dask, Flink and DataFlow

pVACtools

neusomatic

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

faceswap

Deepfakes Software For All

PyTables

A Python package to manage extremely large amounts of data

neural-networks-and-deep-learning

Code samples for my book "Neural Networks and Deep Learning"

awesome-python-sources

include awesome python sources

DG_paper_public

Matlab code

tcga_example

ghelper

谷歌上网助手手动安装包

mutation-signatures

Create mutation signatures from MAF's, and decompose them into Stratton signatures

cellbase

High-Performance NoSQL database and RESTful web services to access to most relevant biological data

ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants