wangziyue57

personal-website

Code that'll help you kickstart a personal website that showcases your work as a software developer.

seurat

R toolkit for single cell genomics

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

sra-tools

SRA Tools

awesome-multi-omics

List of software packages for multi-omics analysis

roxygen2

Generate R package documentation from inline R comments

microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

MicrobiomeStatPlot

Interpretation and visualization of microbiome charts

DESeq2

Differential gene expression analysis based on the negative binomial distribution

sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

VineCopula

Statistical inference of vine copulas

single-cell-3prime-paper

ieugwasr

R interface to the IEU GWAS database API

classroomNotes

Notes on academic-related things

transformGamPoi

Variance stabilizing transformation for Gamma Poisson distributed data

deep_omics

Repository for Short Course: Deep Learning in Omics

Microbiome-Review-Code-Archive

Data, scripts, and outputs for the npj Biofilms and Microbiomes paper "Analysis of microbial compositions: A review of normalization and differential abundance analysis"

CODA

Compositional Data: Simulation and Analyses

M3D

scientific_python_training

scientific python training with pandas, scipy, and scikit-learn

Rplink

Routines to call PLINK from R

HurdleNormal

Estimation and sampling for multi-dimensional Hurdle models on a Normal density with applications to single-cell co-expression

awesome-single-cell

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

XMRF

:exclamation: This is a read-only mirror of the CRAN R package repository. XMRF — Markov Random Fields for High-Throughput Genetics Data. Homepage: http://www.liuzlab.org/XMRF/

mediateR

direct and indirect effect mediation analysis with linear, logistic, and cox models

countgmifs

:exclamation: This is a read-only mirror of the CRAN R package repository. countgmifs — Discrete Response Regression for High-Dimensional Data

mpath

:exclamation: This is a read-only mirror of the CRAN R package repository. mpath — Regularized Linear Models. Homepage: https://github.com/zhuwang46/mpath Report bugs for this package: https://github.com/zhuwang46/mpath

ZIBBSeqDiscovery

:exclamation: This is a read-only mirror of the CRAN R package repository. ZIBBSeqDiscovery — Zero-Inflated Beta-Binomial Modeling of Microbiome Count Data