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beeline

BEELINE: evaluation of algorithms for gene regulatory network inference

dosorio

dosorio.github.io

gene613

Homeworks and Exams

gene638

Homeworks and Exams

l1000-tnbc

Supporting information for "Drug combination prediction for cancer treatment using disease-specific drug response profiles and single-cell transcriptional signatures"

lcl_scrna-seq

scRNA-seq with LCLs - Three cell line samples sequenced: (1) GM12878, (2) GM18502, and (3) the 1:1 mixture of the two

manifoldwarping

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

manuscripts

masterthesis

Identifying proteins and metabolic pathways associated with the neuroprotective response mediated by tibolone in astrocytes under an induced inflammatory model.

milor

R package implementation of milo for testing differentially abundant neighbourhoods

mtproportion

Supporting information for 'Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA sequencing data quality control'

peptides

An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.

rpanglaodb

An R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database into a Seurat object.

rtensor

rTensor v1.2

scorpion

Supplementary information for "Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomic data"

sctransferlearning

Supporting information for "Drug combination prioritization for cancer treatment using single-cell RNA-seq based transfer learning"

stat636

Homeworks

stat646

supercell

Coarse-graining of large single-cell RNA-seq data into super-cells

undergraduatethesis

Analysis of potential membrane disruption and stability of antimicrobial cationic peptides by molecular dynamics simulations

utilities

Some functions in R

vibs613

Homeworks