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atacseq

ATAC-seq peak-calling, QC and differential analysis pipeline

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

clusterprofiler

:bar_chart: A universal enrichment tool for interpreting omics data

coolbox

Jupyter notebook based genomic data visualization toolkit.

crdscore

dchic

dcHiC: Differential compartment analysis for Hi-C datasets

deepblink

Threshold independent detection and localization of diffraction-limited spots.

deepspot

DeepSpot is a deep learning method for the enhancement of mRNA fluorescent spots in microscopy images

detectron2

Detectron2 is a platform for object detection, segmentation and other visual recognition tasks.

diff_tad_type

Analysis the type of diff_tad which from HicExplorer tools HicDifferentialTAD

eg-react

WashU Epigenome Browser

fanc

FAN-C: Framework for the ANalysis of C-like data

htsanalyzer2

HTSanalyzeR2: A R package for gene set enrichment and network analysis of various high-throughput data

imjoy

ImJoy: Deep Learning Made Easy!

juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

mask2former

Code release for "Masked-attention Mask Transformer for Universal Image Segmentation"

mgescore

CellType Definition by Marker Genes Expression

microimageanalysis

measure fluorescence intensities of Hoechst and CENP-F in the nuclei

mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

npzviewer

npzviewer is a simple app to view .npz files from numpy

oneformer

[Preprint] OneFormer: One Transformer to Rule Universal Image Segmentation, 2022

openai-translator

基于 ChatGPT API 的划词翻译浏览器插件和跨平台桌面端应用 - Browser extension and cross-platform desktop application for translation based on ChatGPT API.

python-for-bioimage-analysis

This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biological imaging.

pytorch-unet

PyTorch implementation of the U-Net for image semantic segmentation with high quality images

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

rs-fish

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

sim-fish

Toolbox to simulate smFISH images.

spatiainsituplots

Spatial InSitu plot including gene expression and cell type

spatialimmunocircle

Computing spatial variations around specific cell clusters in the immune microenvironment