hycai's repositories
SpatiaInSituPlots
Spatial InSitu plot including gene expression and cell type
Spatialspots
This document explains how to use three functions to calculate kernel density estimation (KDE), Moran's I statistic, Correlation, Wasserstein distance.
SpatialImmunoCircle
Computing spatial variations around specific cell clusters in the immune microenvironment
diff_tad_type
Analysis the type of diff_tad which from HicExplorer tools HicDifferentialTAD
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
dcHiC
dcHiC: Differential compartment analysis for Hi-C datasets
deepBlink
Threshold independent detection and localization of diffraction-limited spots.
detectron2
Detectron2 is a platform for object detection, segmentation and other visual recognition tasks.
MicroimageAnalysis
measure fluorescence intensities of Hoechst and CENP-F in the nuclei
eg-react
WashU Epigenome Browser
fanc
FAN-C: Framework for the ANalysis of C-like 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"
MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
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.
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.
scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
sim-fish
Toolbox to simulate smFISH images.
Swin-Unet
The codes for the work "Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation"
tackPlotR
A R package to visualize bigwigs.
transit
Repository for the TRANSIT and TPP tools developed by the Ioerger Lab
U-FISH
Deep learning based spot detection for FISH images.