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benchmarking-integration-of-differential-expression

best-of-ml-python

🏆 A ranked list of awesome machine learning Python libraries. Updated weekly.

bimir

BiMiR is a bicluster database that provides the condition-specific microRNA target predictions.

cellenrich

Pathway enrichment analysis / visualize for Single Cell Data

cfiles

A ncurses file manager written in C with vim like keybindings

conquer_comparison

Code for evaluation of differential expression methods in single-cell RNA-seq data

convnext

Code release for ConvNeXt model

desc

Deep Embedding for Single-cell Clustering

distribution-is-all-you-need

The basic distribution probability Tutorial for Deep Learning Researchers

dmmn

Deep Multi-Magnification Network for multi-class tissue segmentation of whole slide images

foresc

single-cell project

glmgampoi

Fit Gamma-Poisson Generalized Linear Models Reliably

gpt-llm-trainer-scgpt

gsasnp2

GSA-SNP2 is successor of GSA-SNP (Nam et al. 2010, NAR web server issue). GSA-SNP2 accepts human GWAS summary data (rs numbers, p-values) or gene-wise p-values (possibly obtained from VEGAS or GATES) and outputs pathway gene sets ‘enriched’ with genes associated with the given phenotype.

hellinger-distance-between-2-gaussian-distributions

Estimate the distance between data clusters by Hellinger's difference

lgtv_wt_ifnar_10x

Single nuclei RNA seq (10x) of cerebral cortex of LGTV infected C57BL/6 WT and Ifnar-/- mice

llama-from-scratch

Llama from scratch, or How to implement a paper without crying

ltmgsca

mlops-zoomcamp

Free MLOps course from DataTalks.Club

mutils_panoptic

Amgad M, Salgado R, Cooper LA. A panoptic segmentation approach for tumor-infiltrating lymphocyte assessment: development of the MuTILs model and PanopTILs dataset. medRxiv 2022.01.08.22268814.

nocodeseg

🔬 Code-free deep segmentation for computational pathology

noobcoding

noobcoding.github.io

pathology-hooknet

pathomicfusion

Fusing Histology and Genomics via Deep Learning - IEEE TMI

python

All Algorithms implemented in Python

scgnn

scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks

scipenn_codes

typical python environment setup

scvi-tools

Deep probabilistic analysis of single-cell omics data

uni

Towards a general-purpose foundation model for computational pathology - Nature Medicine