Single Cell Computational Genomics

Single Cell Computational Genomics's repositories

Nebulosa

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

Language:R80 5 24

scPred

scPred package for cell type prediction from scRNA-seq data

Language:RMIT71 5 28

DropletQC

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

Language:RNOASSERTION31 6 12

onek1k_phase1

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

Language:R23 3 3

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.

Language:Shell14 3 1

CROP-seq

Repository for the processing and analysis of CROP-seq data

Language:R5 20

PEER_factors

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

Language:RGPL-3.05 20

sc-veQTL

Analysis code for sc-veQTL study

Language:RGPL-3.04 20

CellRankJupyter

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

Language:Dockerfile2 10

DropletQC_paper

Analysis code and figures for the DropletQC manuscript

Language:R2 10

Nebulosa_Rv3

Compatible package with older R versions

Language:R200

onek1k_dea

Characterization of transcriptional heterogeneity in OneK1K project

Language:R2 30

Braque

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

Language:RNOASSERTION1 20

iPSC_Village_scripts

scripts used to analyze the iPSC village project

Language:R1 20

OneK1K-Web-browser

Language:HTML1 30

Powell_lab_resources

A public GitHub repo to share resources for common computational challenges

MIT1 20

SingularityBaseImages

Singularity base images that will be build on singularity hub and can be used to build other images

1 20

ancestry_prediction_scRNAseq

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

Language:Python010

Demuxafy_manuscript

Scripts used for manuscript for Demuxafy

Language:RMIT010

fusion_twas

methods for functional summary-based imputation

Language:RGPL-3.0010

gatk4-rnaseq-germline-snps-indels

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

Language:WDLBSD-3-Clause010

hypothalamus_organoid_scRNA

Code used to analyze hypothalamus organoid single cell RN

Language:R010

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

Language:Python010