Pinned Repositories
AIRLOCALIZE
Software for spot detection
bioanalyze-docker-images
Docker Images for Jupyterhub + Bioinformatics
DNAbarcodes
Simple generator of DNA barcodes for sequencing experiments
EASI-FISH
Tools and scripts for EASI-FISH image data analysis
elastix
Official elastix repository
FISHscale
Spatial analysis of FISH data
metacell
Metacell - Single-cell mRNA Analysis
postcode
Decoding of image-based spatial transcriptomics
qupath-extension-warpy
ImgLib2 RealTransform brought to QuPath
starfish
starfish: unified pipelines for image-based transcriptomics
lbgbox's Repositories
lbgbox/AIRLOCALIZE
Software for spot detection
lbgbox/bioanalyze-docker-images
Docker Images for Jupyterhub + Bioinformatics
lbgbox/EASI-FISH
Tools and scripts for EASI-FISH image data analysis
lbgbox/postcode
Decoding of image-based spatial transcriptomics
lbgbox/2021_Haghighi_submitted
High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
lbgbox/AstroPathPipeline
lbgbox/DenoiSeg
Joint training of denoising and segmentation.
lbgbox/labs
Scripts for HarvardX courses: PH525x
lbgbox/NeighborhoodCoordination
Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front"
lbgbox/PuckCaller
Matlab package for image processing and base calling
lbgbox/rasp-mibi
Computational pipeline for multiplexed analysis of tumors.
lbgbox/rearrr
Rearrrange data by a set of methods
lbgbox/REDSEA
lbgbox/scVI
A deep generative model for gene expression profiles from single-cell RNA sequencing
lbgbox/SpatialScore
R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma".
lbgbox/ST-Net
Deep learning on histopathology images.
lbgbox/storm-analysis
STORM movie analysis code
lbgbox/vortex
VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release: