meijian Goto Github PK

normpy

Normalization methods for RNA-Seq expression data in Python.

onek1k_phase1

Contains code to analyze the OneK1K data and perform eQTL mapping of 14 cell types

openslide

C library for reading virtual slide images

pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

palmerpenguins

A great intro dataset for data exploration & visualization (alternative to iris).

pathcnn

Pathology image classifier architecture

pathfinder

pathomicfusion

Fusing Histology and Genomics via Deep Learning - IEEE TMI

personalizedmedicine

A kaggle competition to predict cancer mutation categories using scientific papers

pgx

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

plip

Pathology Language and Image Pre-Training (PLIP) is the first vision and language foundation model for Pathology AI. PLIP is a large-scale pre-trained model that can be used to extract visual and language features from pathology images and text description. The model is a fine-tuned version of the original CLIP model.

public-resources

Repository for resources we'd like to share with the community.

python-dlpy

The SAS Deep Learning Python (DLPy) package provides the high-level Python APIs to deep learning methods in SAS Visual Data Mining and Machine Learning. It allows users to build deep learning models using friendly Keras-like APIs.

python-louvain

Louvain Community Detection

qtlmap

Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue

quasi

List of QuPath scripts for alignment and stain deconvolution of whole-slide histology images

regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.

release

Deep Reinforcement Learning for de-novo Drug Design

rna-seq

rnarry

Simple tools for data analysis for molecular biology of RNA

rnasequest

robust-pca

A simple Python implementation of R-PCA

rtg-tools

RTG Tools: Utilities for accurate VCF comparison and manipulation

rtools

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scina

SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples

scpred

scPred package for cell type prediction from scRNA-seq data

seurat

R toolkit for single cell genomics

signacx

Signac