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ancestry_prediction_scrnaseq

Use SNP genotype information pulled from single cell RNA-seq data to predict ancestries

ascend

Analysis of Single Cell Expression, Normalization and Differential expression

bgi_vs_illumina_benchmark

This repository contains code related to the publication "Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing" by Senabouth et al.

braque

Braque provides a collection of methods to perform pseudo-bulk analysis from single-cell data.

cellrankjupyter

Dockerfile for Cell Rank Jupyter notebooks - includes scanpy, velocyto, scvelo and CellRank

crop-seq

Repository for the processing and analysis of CROP-seq data

demuxafy_manuscript

Scripts used for manuscript for Demuxafy

dropletqc

Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data

dropletqc_paper

Analysis code and figures for the DropletQC manuscript

fusion_twas

methods for functional summary-based imputation

gatk4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools

generic

hypothalamus_organoid_scrna

Code used to analyze hypothalamus organoid single cell RN

imputation_pipeline

Imputation workflow with sanger impuation server, originally prepared for sceQTL-Gen consortium but copied here on 30 August, 2021 when updating to hg38 for sceQTL-Gen consortium

ipsc_village_publication

ipsc_village_scripts

scripts used to analyze the iPSC village project

nebulosa

R package to visualize gene expression data based on weighted kernel density estimation

nebulosa_rv3

Compatible package with older R versions

onek1k-web-browser

onek1k_dea

Characterization of transcriptional heterogeneity in OneK1K project

onek1k_phase1

Contains code to analyze the OneK1K data and perform eQTL mapping of 14 cell types

peer_factors

Contains analysis code to generate PEER factors from pseudo-bulk data and perform eQTL association analysis

plasmablasts_and_neutrophils

powell_lab_resources

A public GitHub repo to share resources for common computational challenges

qtl_to_predictdb

rpe_scrna_agedstudy

Public repository for code related to the generation and analysis of iPSC-derived retina pigmented epithelium cells by Lidgerwood et al.

sc-veqtl

Analysis code for sc-veQTL study

scexplore

R package for single-cell data visualization

scpred

scPred package for cell type prediction from scRNA-seq data

singlecell_prediction

This repo is for predicting cell types using gene expression features