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/CompositeDriver
Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
mil2041/ABIS
mil2041/awesome-community-detection
A curated list of community detection research papers with implementations.
mil2041/awesome-interpretable-machine-learning
mil2041/benchmarking_variant_callers
In this study, we perform systematic comparative analysis of seven widely-used SNV-calling methods, including SAMtools, the GATK Best Practices pipeline, CTAT, FreeBayes, MuTect2, Strelka2 and VarScan2, on both simulated and real single-cell RNA-seq datasets. We evaluate the performances of these tools in different read depths, genomic contexts, functional regions and variant allele frequencies.
mil2041/biological-network-analysis-review
collection of biological network analysis methods
mil2041/biotools
A list of useful bioinformatics resources
mil2041/bulk-rna-seq-review
collections of bulk rna-seq papers
mil2041/cancer-subtype-clustering
collections of cancer subtype clustering methods
mil2041/cellassign
Automated, probabilistic assignment of cell types in scRNA-seq data
mil2041/cheminformatics-tools
collections of cheminformatics tools
mil2041/computational-biology-postdoc-fellowship
collections of computational biology postdoc fellowship
mil2041/ConsensusTME
ConsensusTME Gene Sets and R Script
mil2041/coregistration
Use Jupyter Notebook "coregistration pipeline no imzml.ipynb" from the repository below to co-register your MALDI MSI and fluorescent microscopy images! Use ion_maker.py to produce ion images from your imzML files. More in the readme below!
mil2041/deep-learning-summer-schools
collection of deep learning summer schools
mil2041/developer-roadmap
Roadmap to becoming a web developer in 2020
mil2041/EdMot
An implementation of "EdMot: An Edge Enhancement Approach for Motif-aware Community Detection" (KDD 2019)
mil2041/GTEx_infil
Demographic and genetic factors influence the abundance of infiltrating immune cells in human tissues
mil2041/HAMFA
Hypoxia associated molecular feature analysis
mil2041/HiC_tools
A collection of tools for Hi-C data analysis
mil2041/ImmClass2019
mil2041/MCPcounter
mil2041/MutSpot
mil2041/ngs-structural-variations-review
collections of structural variations tools
mil2041/nlp-roadmap
ROADMAP(Mind Map) and KEYWORD for students those who have interest in learning NLP
mil2041/qvalue
R package to estimate q-values and false discovery rate quantities.
mil2041/react-ui-collections
collections of react ui component
mil2041/Single-Cell-Metabolic-Landscape
Pipeline for exploring metebolic heterogeneity at single-cell resolution
mil2041/single-cell-rnaseq-analysis
A guide for analyzing single-cell RNA-seq data using the R package Seurat. Go from raw data to cell clustering, identifying cell types, custom visualizations, and group-wise analysis of tumor infiltrating immune cells using data from Ishizuka et al. Nature 2019.
mil2041/TIDEpy
TIDE (Tumor Immune Dysfunction and Exclusion), a gene expression biomarker to predict the clinical response to immune checkpoint blockade in Python.