Software

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All Single-cell RNA sequencing Mendelian Randomization Multiple Testing Deep Learning Factor Analysis

VITAE

A Python package to jointly perform trajectory inference for multiple single-cell RNA sequencing datasets. Paper.

GRAPPLE

An R package for Mendelian Randomization (MR), which features the detection of mutliple pleiotropic pathways, the direction of causation and multivariate MR. Paper

adaFilter

An R package for finding mutliple replicating signals under the Partial Conjunction framework. adaFilter can simultaneously find all signals that replicate in at least $r$ out of $n$ studies. Paper

SAVER-X

An R package for denoising scRNA-seq observed UMI counts by transfer learning from existing scRNA-seq datasets. We also provide an open-to-public science Gateway for online computation. Paper

MR.RAPS

An R package for two-sample summary data Mendelian Randomization (MR) using the robust adjusted profile score. Paper

DESCEND

An R package to estimate the underlying true gene expression distributions for each gene and a given cell group from noisy scRNA-seq observed UMI counts. DESCEND can also find genes whose dispersion (variance, Gini coefficient) change between cell groups. Paper

CATE

An R package using a linear factor model to perform valid inference after adjust for hidden confounding factors Paper

esaBcv

An R package to estimate the number of factors in factor analysis using bi-cross-validation. Paper