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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 modelminerva-author-ui
Minerva Author is an authoring tool used to create Minerva narrated stories via selection of specific channel groupings and image views.morgancpp
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
scn2ometiff
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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