# Projects

## VITAE

A Python package to jointly perform trajectory inference for multiple single-cell RNA sequencing datasets. [Paper](https://jingshuw.org/publication/du-2020-aa/).

## GRAPPLE

An R package for Mendelian Randomization (MR), which features the detection of mutliple pleiotropic pathways, the direction of causation and multivariate MR. [Paper](https://jingshuw.org/publication/wang-2020-aa/)

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](https://jingshuw.org/publication/wang-2020-detecting/)

## 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](https://singlecellgateway.wharton.upenn.edu/) for online computation. [Paper](https://jingshuw.org/publication/wang-2018-aa/)

## MR.RAPS

An R package for two-sample summary data Mendelian Randomization (MR) using the robust adjusted profile score. [Paper](https://jingshuw.org/publication/zhao-2020-aa/)

## 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](https://jingshuw.org/publication/wang-2018-aa/)

## CATE

An R package using a linear factor model to perform valid inference after adjust for hidden confounding factors [Paper](https://jingshuw.org/publication/wang-2017-aa/)

## esaBcv

An R package to estimate the number of factors in factor analysis using bi-cross-validation. [Paper](https://jingshuw.org/publication/owen-2016-aa/)