zhaojk Goto Github PK

2019_strunz

Reproducibility repo accompanying Strunz et al. "Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis". Nat Commun. 2020.

analyzeskeleton

ImageJ/Fiji plugin to analyze 2D and 3D skeleton images

animateddrawings

Code to accompany "A Method for Animating Children's Drawings of the Human Figure"

autospill

R package: AutoSpill algorithm for calculating spillover coefficients to compensate or unmix high-parameter flow cytometry data

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

bark

🔊 Text-Prompted Generative Audio Model

batch-adjust-warning-figures

batch-effect-removal-benchmarking

A benchmark of batch-effect correction methods for single-cell RNA sequencing data

cellchat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

cellpose

a generalist algorithm for cellular segmentation

cellranger

10x Genomics Single Cell 3' Gene Expression and VDJ Assembly

celltypist

A tool for semi-automatic cell type annotation

cellxgene

An interactive explorer for single-cell transcriptomics data

cellxgenevip_docker

install cellxgeneVIP in docker

chineseocr_lite

超轻量级中文ocr，支持竖排文字识别, 支持ncnn、mnn、tnn推理 ( dbnet(1.8M) + crnn(2.5M) + anglenet(378KB)) 总模型仅4.7M

clustermap

ClusterMap is an R package to analyze and compare two or more single cell expression datasets.

codehub

CodeHub is the best way to browse and maintain your GitHub repositories on any iOS device!

collectcodes

Personel collected codes

compass

In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes

compass_apptainer

apptainer image for compass

covid_meta_analysis

Analysis notebooks for the Covid-19 meta analysis that accompanies the Nature Medicine publication "Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics"

czitools

Small python package to simplify reading CZI Image Metadata (*.czi)

dagdata

Data for the HarvardX courses: PH525x

data-carpentry-rnaseq

deseq2

Differential gene expression analysis based on the negative binomial distribution

dropseq_personel

Pipeline to process DROP-seq data

extended-single-cell-best-practices-container

Hosting the container for the extended single-cell best-practices book

fascia_calcium_scoring

Code for evaluate swelling and contraction score across fibroblasts; Code for evaluating calcium intensity in cultured fascia in vitro

fetch_srr

Download SRR in batch with snakemake

fiji_script_repo

This is a test