mil2041
Postdoc at MSKCC studying cancer systems biology.
Memorial Sloan Kettering Cancer CenterNew York City
Pinned Repositories
2020_Wilk_COVID
Reproducibility repository accompanying Wilk, Rustagi, Zhao, et al. "A single-cell atlas of the peripheral immune response to severe COVID-19"
ABIS
academic_writing
academic writing
ADAM
Adaptive Daisy Model to discriminate core-fitness/context-specific essential genes in large scale CRISPR-Cas9 screens
Aneuploidy_dependencies
scripts for plots
AutoGeneS
CNCDatabase
A full stack web app for querying cancer driver evidences curated from literature
CNCDriver
Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
CompositeDriver
Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
netboxr
An R package to mark functional modules in the network analysis using data from pathwayCommons
mil2041's Repositories
mil2041/academic_writing
academic writing
mil2041/AutoGeneS
mil2041/bayestme
BayesTME: A reference-free Bayesian method for analyzing spatial transcriptomics data
mil2041/bisque
An R toolkit for estimation of cell composition from bulk expression data
mil2041/Code_Request
General R functions and scripts for publications
mil2041/COSMOS
mil2041/DeepDRIM
mil2041/DeepIMV
A Variational Information Bottleneck Approach to Multi-Omics Data Integration
mil2041/FiDEL
R library - A binary classifier based on the class probability at a given rank following Fermi-Dirac distribution
mil2041/Genoppi
Genoppi: an open-source software for robust and standardized integration of proteomic and genetic data
mil2041/immunedeconv
A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter)
mil2041/Imputation
mil2041/liger
R package for integrating and analyzing multiple single-cell datasets
mil2041/Mask_RCNN
Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow
mil2041/ML-radiation
Machine learning prediction of tumor radiation response from multi-omics TCGA data
mil2041/mljar-supervised
Automated Machine Learning Pipeline with Feature Engineering and Hyper-Parameters Tuning :rocket:
mil2041/mtdna-mutations
scripts to generate figures/tables from Gorelick et al. Nat Metab, 2021
mil2041/Nuc2Vec
mil2041/og-aws
📙 Amazon Web Services — a practical guide
mil2041/Pan-Cancer-Nuclei-Instance-Segmentation
Instance Segmentation of 5 Different Cancer Nuclei Across 19 Unique Tissue Types
mil2041/PANOPLY
Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
mil2041/python-bioimage-analysis-tutorial
The new and improved 2018 version of the EMBL Python BioImage Analysis Tutorial. Now finally in python 3!
mil2041/RNAsum
Pipeline for generating RNAseq-based cancer patient reports
mil2041/sc-pert
Models and datasets for perturbational single-cell omics
mil2041/scPred
scPred package for cell type prediction from scRNA-seq data
mil2041/shannonca
Information-based dimensionality reduction
mil2041/SigProfilerExtractor
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
mil2041/singleCellNet
SingleCellNet: classify single cells across species and platforms
mil2041/ST-Net
Deep learning on histopathology images.
mil2041/system-design-primer
Learn how to design large-scale systems. Prep for the system design interview. Includes Anki flashcards.