mil2041

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/awesome-dg-cpath

Awesome Domain Generalization for Computational Pathology

mil2041/Awesome-Foundation-Models-in-Medical-Imaging

A curated list of foundation models for vision and language tasks in medical imaging

mil2041/Awesome-Information-Bottleneck

This is a curated list for Information Bottleneck Principle, in memory of Professor Naftali Tishby.

mil2041/awesome-kan

A comprehensive collection of KAN(Kolmogorov-Arnold Network)-related resources, including libraries, projects, tutorials, papers, and more, for researchers and developers in the Kolmogorov-Arnold Network field.

mil2041/awesome-scalability

The Patterns of Scalable, Reliable, and Performant Large-Scale Systems

mil2041/CaRAS

An Integrated Analysis Pipeline for Unbiased CUT&RUN/CUT&Tag Analysis

mil2041/Cell-Vision-Fusion

A SwinV2 transformer-based fusion approach combining Cell Painting images, image-based profiles and compound structures to predict kinase inhibitor mechanism of action.

mil2041/computational-biology-conferences

curated list of computational biology conferences

mil2041/data-to-paper

data-to-paper: Backward-traceable AI-driven scientific research

mil2041/DinoBloom

Blood Cell Foundation Model based on DINOv2

mil2041/dinov2-finetune

Finetuning DINOv2 (https://github.com/facebookresearch/dinov2) on your own dataset

mil2041/EPInformer

code to run EPInformer for gene expression prediction and gene-enhancer links prioritization

mil2041/FR-Perturb

Factorize-Recover for Perturb-seq analysis (FR-Perturb)

mil2041/hd_wsi

mil2041/HGSOC_platinum_response

Code for the manuscript "Histopathology and proteomics are synergistic for High-Grade Serous Ovarian Cancer platinum response prediction"

mil2041/HiC_data

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

mil2041/Histopathology-Datasets

Ressources of histopathology datasets

mil2041/HSPH_scRNA_20241023

mil2041/IMC-IF

Dual-modality imaging of immunofluorescence and imaging mass cytometry for high-resolution whole slide imaging with accurate single-cell segmentation

mil2041/LLM101n

LLM101n: Let's build a Storyteller

mil2041/LLMs-in-science

mil2041/MultiModalBrainSurvival

mil2041/MultimodalPathologySearch

mil2041/nichenetr

NicheNet: predict active ligand-target links between interacting cells

mil2041/PathOmics

[MICCAI 2023 Oral] The official code of "Pathology-and-genomics Multimodal Transformer for Survival Outcome Prediction" (top 9%)

mil2041/SAM4MIS

SAM & SAM 2 for Medical Image Segmentation: Open-Source Project Summary

mil2041/scRNA-seq_notes

A list of scRNA-seq analysis tools

mil2041/scSpaMet

mil2041/SPLICE

Patch Collage Generator

mil2041/Transformers-Tutorials

This repository contains demos I made with the Transformers library by HuggingFace.