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ashlar
ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registrationmcmicro
Multiple-choice microscopy pipelinescimap
Spatial Single-Cell Analysis Toolkitminerva-story
Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.minerva_analysis
cylinter
An Interactive Image Segmentation Filter for Multiplex Microscopypalom
Piecewise alignment for layers of mosaicsvisinity
smallmoleculesuite-old
minerva-author
Tool to create images and configuration files for Minerva-Storyome-tiff-pyramid-tools
Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.scope2screen
Scope2Screen is an open-source web-application for focus+context exploration and annotation of whole-slide, high-plex, tissue images.DRIADrc
Resources for Drug Repurposing In Alzheimer's Disease (DRIAD) workCRC_atlas_2022
orion-crc
quantification
Quantification module for mcmicroDRIAD
Drug Repurposing in Alzheimer's Diseasebasic-illumination
ImageJ BaSiC shading correction for use with Ashlarnaivestates
Inference of cell states using Naive Bayessmallmoleculesuite
cluequery
An R interface to the Connectivity Map API at clue.ioredseapy
lsp-cheminformatics
API for performing all kinds of cheminformatics task, like fingerprinting and chemical similarity computationsKinCo
Kinase-compound affinity prediction based on structuresminerva-browser
marm2-supplement
Supplementary Material for the MARM2.0 modelmorgancpp
Efficient structure for storing and comparing Morgan fingerprintsdubportal
An integrative resource for deubiquitinating enzymes (DUBs) served at https://labsyspharm.github.io/dubportalmarm1-supplement
Supplemental code and model files for the MARM1 model publication, Gerosa et al.harvardtissueatlas
Harvard Tissue Atlas websitePanFab-PAPR-2021
Greater Boston Pandemic Fabrication Team Powered Air-Purifying Respirator (PanFab PAPR)UnMICST-info
cycif.org
cycif.org GitHub Pages Websitescn2ometiff
Convert a Leica .SCN file to OME-TIFF formatminerva-lib-python
Minerva Python LibraryOMERO_scripts
Repository for OMERO related scriptsvae-paper
cellcutter
Create thumbnails of cells in a given image.rnaseq
Guide for aligning deep RNAseq and Digital Gene Expression (DGE) reads using bcbio.minerva-cloud
Minerva Cloud is a novel cloud-native (AWS) platform for high-dimensional microscopy image storage, management, and visualization.sms-maintenance
Scripts for maintaining and processing Small Molecule Suite data.selectivity_comparisons
enrichr.db
Data package providing gene sets from Enrichr in Rcd73_coy_spatialcorrelation
driad-website
Web app for Drug Repurposing in Alzheimer's Diseaselincs_proteomics_data_descriptor
This repository includes code used to process and visualize datasets that feature in the LINCS proteomics data descriptordark-kinome-old
aws-tools
General purpose scripts for managing our AWS usagepalmer-plana-2020
lymphonet_2023
Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinomadigipath_ml
mcmicro-ilastik
Ilastik segmentation module for mcmicroludwigtumoratlas.org
Ludwig Tumor Atlas websitepamsig
Partitioning Around Medoids (PAM) and generation of cluster SIGnaturesmcmicro-scanpy
An MCMICRO module implementation of scanpy for clustering cellslspci
A site describing LSP compounds served at https://labsyspharm.github.io/lspci/bfextractor
npjbcancer2023
Scripts and data for NPJ Breast Cancer 2023 (Guerriero-Lin-Santagata)cylinter-paper
kinome-website
tissue_integrity_dashboard
Interactive dashboard showing DNA correlation coefficient as indicator of tissue integrity at single cell levelminerva-cli
Minerva Command Line Interfacebfscanner
Bio-Formats Directory Scannerminerva-cloud-ui
Minerva Cloud is a novel cloud-based (AWS) software for high-dimensional image management, storage and visualization.gater
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