Explore @labsyspharm Open Source projects

Laboratory of Systems Pharmacology @ Harvard (@labsyspharm)

labsyspharm

Stars
631
Global Org. Rank 20,713 (Top 7 %)
Registered almost 6 years ago
Most used languages

Python
33.8 %

R
21.5 %

JavaScript
12.3 %

Jupyter Notebook
6.2 %

MATLAB
6.2 %

HTML
6.2 %

SCSS 3.1 %

Nextflow 1.5 %

Java
1.5 %

CSS
1.5 %

C
1.5 %

C++
1.5 %

Shell
1.5 %

Mathematica 1.5 %
Location 🇺🇸 United States
Country Total Rank 15,504
Country Ranking

Nextflow 2

Mathematica 664

R
718

MATLAB
885

SCSS 908

HTML
2,726

Python
3,867

ashlar

ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration

mcmicro

Multiple-choice microscopy pipeline

scimap

Spatial Single-Cell Analysis Toolkit

minerva-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 Microscopy

palom

Piecewise alignment for layers of mosaics

visinity

smallmoleculesuite-old

minerva-author

Tool to create images and configuration files for Minerva-Story

ome-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) work

CRC_atlas_2022

orion-crc

quantification

Quantification module for mcmicro

DRIAD

Drug Repurposing in Alzheimer's Disease

basic-illumination

ImageJ BaSiC shading correction for use with Ashlar

naivestates

Inference of cell states using Naive Bayes

smallmoleculesuite

cluequery

An R interface to the Connectivity Map API at clue.io

redseapy

lsp-cheminformatics

API for performing all kinds of cheminformatics task, like fingerprinting and chemical similarity computations

KinCo

Kinase-compound affinity prediction based on structures

minerva-browser

marm2-supplement

Supplementary Material for the MARM2.0 model

minerva-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 fingerprints

dubportal

An integrative resource for deubiquitinating enzymes (DUBs) served at https://labsyspharm.github.io/dubportal

marm1-supplement

Supplemental code and model files for the MARM1 model publication, Gerosa et al.

Jupyter Notebook

harvardtissueatlas

Harvard Tissue Atlas website

PanFab-PAPR-2021

Greater Boston Pandemic Fabrication Team Powered Air-Purifying Respirator (PanFab PAPR)

UnMICST-info

cycif.org

cycif.org GitHub Pages Website

scn2ometiff

Convert a Leica .SCN file to OME-TIFF format

minerva-lib-python

Minerva Python Library

OMERO_scripts

Repository for OMERO related scripts

vae-paper

Jupyter Notebook

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 R

cd73_coy_spatialcorrelation

driad-website

Web app for Drug Repurposing in Alzheimer's Disease

lincs_proteomics_data_descriptor

This repository includes code used to process and visualize datasets that feature in the LINCS proteomics data descriptor

dark-kinome-old

aws-tools

General purpose scripts for managing our AWS usage

palmer-plana-2020

lymphonet_2023

Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma

digipath_ml

mcmicro-ilastik

Ilastik segmentation module for mcmicro

ludwigtumoratlas.org

Ludwig Tumor Atlas website

pamsig

Partitioning Around Medoids (PAM) and generation of cluster SIGnatures

mcmicro-scanpy

An MCMICRO module implementation of scanpy for clustering cells

lspci

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

Jupyter Notebook

kinome-website

tissue_integrity_dashboard

Interactive dashboard showing DNA correlation coefficient as indicator of tissue integrity at single cell level

Jupyter Notebook

minerva-cli

Minerva Command Line Interface

bfscanner

Bio-Formats Directory Scanner

minerva-cloud-ui

Minerva Cloud is a novel cloud-based (AWS) software for high-dimensional image management, storage and visualization.

gater