SingleCellAPA_evaluation

Package list

Here is the all package i used to perform performance testing, each package could be install following given steps.

Name	Language	Identification of pA sites	PolyA_USE	Invidual cell matrix	Version	website
MAAPER	R	Modeling based on known PASs	No	No	1.1.1	https://github.com/Vivianstats/MAAPER
scAPA	Shell, R	Homer and mclust::Mclust (R package)	No	Yes	0.1.0	https://github.com/ElkonLab/scAPA
scAPAtrap	R	derfinder::regionMatrix (R package)	Yes; correct pA site	Yes	0.1.0	https://github.com/BMILAB/scAPAtrap
SCAPTURE	Shell	Homer	No	Yes	1	https://github.com/YangLab/SCAPTURE
scDaPars	python	DaPars2	No	No	0.1.0	https://github.com/YiPeng-Gao/scDaPars
Sierra	R	fit a Guassian with NLS or MLE	No	Yes	0.99.27	https://github.com/VCCRI/Sierra
SCAPE	python	Modeling based on fragment size	No	Yes	1.0.0	https://github.com/LuChenLab/SCAPE
polyApipe	python	Soft clipped reads with poly(A)	Yes	Yes	0.1.0	https://github.com/MonashBioinformaticsPlatform/polyApipe

How to use it

Requirement

1. Install all packages were listed above.
2. R (4.0.3)
3. python (3.7.3)
4. snakemake (6.6.1)

Run

snakemake -s simu_run.py

Publication

Zhou et al. SCAPE: A mixture model revealing single-cell polyadenylation diversity and cellular dynamic during cell differentiation and reprogramming.