ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis (Granja JM*, Corces MR*, et al. 2020)

Link : https://www.biorxiv.org/content/10.1101/2020.04.28.066498v1

Please cite : Granja JM et al., An integrative and scalable software package for single-cell chromatin accessibility analysis. bioRxiv (2020)

Brief Descriptions of Analysis Scripts

scATAC Analyses (See Code Folder)

ArchR_Make_Gene_Models.R - Code for making individual gene score models with ArchR.

ArchR_Test_Gene_Score_Model_Aggregates.R - Code for testing gene score models with aggregates of cells.

ArchR_PreProcess_Laptop_SimulatedPBMC_1M.R - Code for benchmarking analysis of 1M Simulated PBMC.

ArchR_PreProcess_Laptop_LargeHeme_220k.R - Code for benchmarking analysis of Large Hematopoeisis.

ArchR_PostAnalysis_Large_Heme_Analysis.R - Code for advanced post analysis of Large Hematopoeisis.

scATAC-seq Files

10x Version1 vs NextGem (Fragment Files) - https://www.10xgenomics.com/solutions/single-cell-atac/

Satpathy+, Granja+ et al 2019 (Fragment Files) - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129785&holding=F1000&otool=stanford

Granja+, Klemm+, McGinnis+ et al 2019 (Fragment Files) - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139369

Buenrostro et al 2018 (Bam Files) - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96772

Cusanovich et al 2018 (Bam Files) - http://atlas.gs.washington.edu/mouse-atac/data/

Benchmarking Results (ArchR, SnapATAC, Signac)

PBMC 10k - https://github.com/GreenleafLab/ArchR_2020/tree/master/ArchR_Benchmarking/PBMC-10k

PBMC 20k - https://github.com/GreenleafLab/ArchR_2020/tree/master/ArchR_Benchmarking/PBMC-20k

PBMC 30k - https://github.com/GreenleafLab/ArchR_2020/tree/master/ArchR_Benchmarking/PBMC-30k

PBMC 70k - https://github.com/GreenleafLab/ArchR_2020/tree/master/ArchR_Benchmarking/PBMC-70k

BMMC 30k - https://github.com/GreenleafLab/ArchR_2020/tree/master/ArchR_Benchmarking/BMMC-30k

Mouse Atlas 70k - https://github.com/GreenleafLab/ArchR_2020/tree/master/ArchR_Benchmarking/MouseAtlas-70k/ArchR

Note 1. We included 1 replicate Rmarkdown for the large computational setup since we have results for all softwares for each of the steps.

Note 2. We merged steps as described in the supplemental of the MS for clarity.

Additional Data Download Links

These links may be moved if we can find a better host for better download speed

Notes

.rds file is an R binarized object to read into R use readRDS(filename)

SummarizedExperiment is a class in R see :
https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html

deviations (TF chromVAR) is a class in R see :
https://bioconductor.org/packages/release/bioc/html/chromVAR.html

Large Hematopoiesis

ArchR Project Containing Arrow Files :
https://drive.google.com/file/d/1L8hOTLDxqdzgqY4hw_uXr5O2m8qd9Bdn/view?usp=sharing

scATAC-seq Hematopoeisis cell x peak Summarized Experiment :
https://drive.google.com/file/d/1zWFJes4z2uMOkgm4kEd7zffjlgBnlSxD/view?usp=sharing

scATAC-seq Hematopoeisis cell x motif Summarized Experiment :
https://drive.google.com/file/d/1RUOcJbxric6PF3Ilzx4622uS2Lbi8r31/view?usp=sharing