mairenileath

mutex

A package for finding mutually exclusive and co-occurring pairs and triplets of mutations.

coffdrop

Comprehensive toolkit for mutual exclusivity and co-occurrence analysis of cancer mutations.

microbe

The-world-of-faculty

resources for faculty

battenberg

Battenberg R package for subclonal copynumber estimation

martin_et_al_cell_2019

Scripts and data files used to generate the figures of the Crohn's single-cell RNA-seq paper "Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy"

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

JaBbA

MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.

nichenetr

NicheNet: predict active ligand-target links between interacting cells

fishHook

R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.

octopus

Bayesian haplotype-based mutation calling

teaching

My teaching materials.

B-cells-scRNAseq-in-BC

Bio-10X

Use Seurat,monocle etc in R to analysis 10X single cell dataset

HCA_skin

HCA data analysis

10x-scATAC-2019

Publication Page for Satpathy*, Granja* et al 2019

ggbump

A geom for ggplot to create bump plots

single-cell-3prime-paper

kallistobustools

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

tenx

Pipelines for the analysis of 10x single-cell RNA-sequencing data

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

Integration2019

scRNA-seq

placental-villous-explants-scRNAseq

analysis on public scRNAseq data

FootprintMethods_on_scRNAseq

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

besca

BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis

SingleCell_template

single cell RNA-seq analysis template based on online resources