Pinned Repositories
3D_IMC_publication
ACDC_tutorial
airlab
Analyze_CyTOF_Using_Seurat
Cytometry by time-of-flight(CyTOF) data is very useful in studying the presence/absence of antigens/surface markers at single cell level. There are multiple tools to analyze CyTOF data but here I am presenting a tutorial of how one can quickly use Seurat (R package for scRNA-Seq analysis) for analyzing CyTOF data and understand the cellular and phenotypic diversity
ark-analysis
Integrated pipeline for multiplexed image analysis
Multicore-opt-SNE
Parallel opt-SNE implementation with Python wrapper
scRNA.seq.course
Analysis of single cell RNA-seq data course
StarXian's Repositories
StarXian/ark-analysis
Integrated pipeline for multiplexed image analysis
StarXian/Balagan
Package for analysis and experimental design of multiplexed imaging data
StarXian/bindSC
Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data
StarXian/cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
StarXian/CellSeg
StarXian/Chinese-Pangenome-Consortium-Phase-I
StarXian/CISA
Computational Immune Synapse Analysis
StarXian/CSBB-Shiny
Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis
StarXian/CyTOF_analysis_Pipeline1
StarXian/CytoQP
StarXian/GarciaVallejoLab
Repository for projects developed within the lab of JJ. Garcia-Vallejo
StarXian/histocat-web
Histology Topography Cytometry Analysis Toolbox (histoCAT) for Web.
StarXian/I2K-Workshop-Materials
StarXian/imc
IMC: Intermodule Communication API
StarXian/imc-1
A package for the analysis of Imaging Mass Cytometry data
StarXian/IMC_DataAnalysis
Simple workflow for IMC data exploration, annotation and visualisation of single-cells
StarXian/Mask_RCNN
Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow
StarXian/napari
napari: a fast, interactive, multi-dimensional image viewer for python
StarXian/napari-imc
Imaging Mass Cytometry (IMC) file type support for napari
StarXian/PhenoComb
An R package for combinatorial analysis of phenotypes
StarXian/phenoptr
Helper functions for working with inForm data.
StarXian/phenoptrReports
Create analysis reports from inForm data.
StarXian/SIMPLI
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
StarXian/Slicer-TITAN
TITAN is responsible for the pre-processing and analysis tasks of imaging mass cytometry (IMC) data. https://doi.org/10.1002/cyto.a.24535
StarXian/SPACEL
StarXian/SPATA2
A Toolbox for Spatial Gene Expression Analysis
StarXian/spicyR
StarXian/squidpy
Spatial Single Cell Analysis in Python
StarXian/SuperPrompt
SuperPrompt is an attempt to engineer prompts that might help us understand AI agents.
StarXian/TissUUmaps
TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used as a web service or locally in your computer, and allows users to share regions of interest and local statistics.