Successful Job Applications and Grants

Inferring CNV from Single-Cell RNA-Seq

MOODS: Motif Occurrence Detection Suite

Graph-linked unified embedding for single-cell multi-omics data integration

Physicochemical properties, indices and descriptors for amino-acid sequences.

Breast Cancer Single Cell Atlas

Methods for combining p-values.

Single cell typing based on cell ontology

A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution methods

Scissor package

Symphony algorithm for inference of cell type specific gene regulatory networks from scRNA-seq and ATAC-seq

RNA-seq aligner

Generalized Random Forests

🎯 Human transcription factor target genes from 6 databases in convenient R format.

BioNetComp: a Python package for biological network development and comparison

Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data

A simulator for single-cell expression data guided by gene regulatory networks

Tidy data frames and expressions with statistical summaries 📜

GeneWalk identifies relevant gene functions for a biological context using network representation learning

R package for non-parametric analysis

A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍

Code for the AAAI 2012 Manifold Warping paper: http://people.cs.umass.edu/~ccarey/pubs/ManifoldWarping.pdf

Lightweight Iterative Gene set Enrichment in R

Ultrafast exhaustive epistasis scan for quantitative traits with covariate adjustment

Table of software for the analysis of single-cell RNA-seq data.

Computational method for Comparative ReConstruction of genome-scale metabolic networks

Intuitive visualization of pharmacometric models' structure, parameters and uncertainty

Graph and network visualization using tabular data in R