qys2007

deep_omics

Repository for Short Course: Deep Learning in Omics

dndscv

dN/dS methods to quantify selection in cancer and somatic evolution

awesome-compose

Awesome Docker Compose samples

analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.

sceasy

A package to help convert different single-cell data formats to each other

msisensor2

Microsatellite instability (MSI) detection for tumor only data.

rapids-single-cell-examples

Examples of single-cell genomic analysis accelerated with RAPIDS

scRNAseq-analysis-notes

scRNAseq analysis notes from Ming Tang

thematic

Theme ggplot2, lattice, and base graphics based on a few simple settings.

scrublet

Detect doublets in single-cell RNA-seq data

solo

software to detect doublets

SignatureAnalyzer

Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.

rsem

Wrapper workflow and Decider for RSEM tool (transcription analysis for RNAseq)

cumulus

Cloud-based scalable and efficient single-cell genomics workflows

deseq2_or_edger

DESeq2 or edgeR

li_et_al_cell_2018_melanoma_scrna

scell_lung_adenocarcinoma

This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset

topiary

Predict mutated T-cell epitopes from sequencing data

portcullis

Splice junction analysis and filtering from BAM files

Intorduction-to-Python-and-Data-Science

PharmCAT

The Pharmacogenomic Clinical Annotation Tool

reproducible-science

material for teaching reproducible science with R and RStudio

ggupset

Combination matrix axis for 'ggplot2' to create 'UpSet' plots

Workshop_Annotation

Course materials for "Variants Annotate and Phenotype Analysis"

disambiguate

Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem

Sargasso

Sargasso disambiguates mixed-species high-throughput sequencing data.

PANGenomics

azimuth

A Shiny web app for mapping datasets using Seurat v4

wrangling-genomics

Data Wrangling and Processing for Genomics

slidify

Generate reproducible html5 slides from R markdown