NIH
LINCS
program
Library of Integrated Network-Based Cellular Signatures
☰
Home
About
Centers
Data
Tools
Community
Publications
News
LINCS Tools Marketplace
Tools and tutorials to help you be more productive with LINCS datasets
LINCS Tools
Marketplace
Video Tutorials
Sort by
Popularity
Filter by
Center
All
Data Type
All
Role
All
Feature
All
Data Type
Transcript Data
Role
Data Analysis
Data Integration
Data Storage
Data Visualization
Network Analysis
Signature Generation
Feature
API
Database
Open Source
Search Engine
Web-based
L1000CDS2
BD2K-LINCS DCIC
An ultra-fast LINCS L1000 Characteristic Direction signature search engine
Data Type
Cell State Data
Drug Binding Data
Protein Data
Role
Data Integration
Data Visualization
Network Analysis
Feature
Documentation
Open Source
Provenance
Web-based
Drug-Pathway Browser
HMS LINCS
Interactive map of key signal transduction pathways and drug-target data
Data Type
Protein Data
Transcript Data
Role
Data Analysis
Data Integration
Data Visualization
Network Analysis
Signature Generation
Feature
API
Database
Ontology
Search Engine
Web-based
iLINCS
BD2K-LINCS DCIC
An integrative web platform for analysis of LINCS data and signatures
Data Type
Cell State Data
Protein Data
Transcript Data
Role
Data Analysis
Data Formatting
Data Integration
Data Storage
Data Visualization
Network Analysis
Signature Generation
Feature
API
Database
Documentation
Ontology
Open Source
Search Engine
Web-based
Enrichr
BD2K-LINCS DCIC
An intuitive web-based gene list enrichment analysis tool with 133 libraries
Data Type
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Visualization
Feature
API
Database
Search Engine
Web-based
Repurposing App
LINCS Transcriptomics
Tool to explore repurposing collection of ~5000 tool compounds and drugs
Data Type
Cell State Data
Drug Binding Data
Role
Data Analysis
Data Formatting
Data Integration
Data Visualization
Feature
Database
Documentation
Search Engine
Web-based
Drug/Cell-line Browser
BD2K-LINCS DCIC
DCB provides interactive visualization of cancer cell-line viability data
Data Type
Cell State Data
Drug Binding Data
Morphology Data
Protein Data
Transcript Data
Role
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Feature
API
Database
Documentation
Ontology
Provenance
Scripting
Search Engine
Versioning
Web-based
LINCS Data Portal
BD2K-LINCS DCIC
Provides unified interface for searching all LINCS dataset packages and entities
Data Type
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Visualization
Network Analysis
Feature
API
Database
Search Engine
Web-based
CLUE Platform
LINCS Transcriptomics
Computational environment to interface with the L1000 data
Data Type
Drug Binding Data
Role
Data Analysis
Data Integration
Data Visualization
Network Analysis
Signature Generation
Feature
API
Database
Open Source
Search Engine
Web-based
L1000FWD
BD2K-LINCS DCIC
Large-scale visualization of drug-induced transcriptomic signatures
Data Type
Transcript Data
Role
Data Analysis
Data Documentation
Data Integration
Signature Generation
Feature
Database
Documentation
Open Source
Search Engine
Web-based
Drug Gene Budger
BD2K-LINCS DCIC
Identifies drugs & small molecules to regulate expression of target genes
Data Type
Cell State Data
Drug Binding Data
Morphology Data
Protein Data
Transcript Data
Role
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Feature
API
Database
Documentation
Ontology
Provenance
Scripting
Search Engine
Versioning
Web-based
SigCom LINCS
BD2K-LINCS DCIC
Provides unified interface for searching over one million signatures
Data Type
Cell State Data
Role
Data Visualization
Signature Generation
Feature
Documentation
Open Source
Provenance
Web-based
Drug Response Browser
HMS LINCS
Online tool for browsing breast cancer cell line drug dose-response data
Data Type
Transcript Data
Role
Data Analysis
Data Visualization
Feature
Search Engine
Web-based
Query App
LINCS Transcriptomics
Connections to user-defined signatures
Data Type
Cell State Data
Morphology Data
Protein Data
Transcript Data
Role
Data Formatting
Data Visualization
Feature
Documentation
Web-based
LINCS Data Explorer
MEP LINCS
Visualization of the MEMA data from the MEP LINCS Center
Data Type
Protein Data
Transcript Data
Role
Data Analysis
Data Integration
Data Visualization
Network Analysis
Feature
Command Line
Open Source
Omics Integrator
NeuroLINCS
Discovers networks linking proteomic, transcriptomic, and epigenomic data
Data Type
Drug Binding Data
Role
Data Analysis
Data Formatting
Data Integration
Data Storage
Feature
Database
Documentation
Open Source
Search Engine
Web-based
Small Molecule Suite
Curated database with drug target data and drug similarity data.
Data Type
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Network Analysis
Signature Generation
Feature
API
Database
Documentation
Open Source
Web-based
GEO2Enrichr
BD2K-LINCS DCIC
A web app and browser extension to extract and analyze signatures from GEO
Data Type
Cell State Data
Drug Binding Data
Morphology Data
Protein Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Network Analysis
Signature Generation
Feature
API
Database
Documentation
Ontology
Open Source
Provenance
Scripting
Search Engine
Versioning
Web-based
Harmonizome
BD2K-LINCS DCIC
Web portal with a collection of 114 datasets abstracted into gene function tables
Data Type
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Network Analysis
Signature Generation
Feature
API
Database
Documentation
Ontology
Search Engine
Web-based
CREEDS
BD2K-LINCS DCIC
Collections of processed gene, drug and disease signatures from GEO
Data Type
Transcript Data
Role
Data Analysis
Data Integration
Data Visualization
Network Analysis
Signature Generation
Feature
Documentation
Open Source
Provenance
TieDIE
HMS LINCS
Software for computing regulatory subnetworks from mutation and transcript data
Data Type
Cell State Data
Drug Binding Data
Morphology Data
Protein Data
Role
Data Integration
Data Visualization
Feature
Ontology
Open Source
Provenance
Search Engine
Web-based
Breast Cancer Browser
HMS LINCS
Online tool for browsing multiple datasets relevant to breast cancer biology
Data Type
Transcript Data
Role
Data Analysis
Data Integration
Signature Generation
Feature
Open Source
Web-based
SynergySeq
BD2K-LINCS DCIC
Identify synergistic drug combinations
Data Type
Cell State Data
Drug Binding Data
Morphology Data
Protein Data
Transcript Data
Role
Data Documentation
Data Formatting
Data Storage
Feature
API
Database
Documentation
Ontology
Open Source
Provenance
Search Engine
Versioning
Web-based
HMS LINCS Database
HMS LINCS
Online database for access to HMS LINCS Center datasets and reagent information
Data Type
Drug Binding Data
Morphology Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Visualization
Network Analysis
Signature Generation
Feature
API
Database
Documentation
Search Engine
Web-based
SEP L1000
BD2K-LINCS DCIC
Web portal for searching and browsing predictive small-molecule/ADR connections
Data Type
Drug Binding Data
Protein Data
Transcript Data
Role
Data Analysis
Data Integration
Data Visualization
Network Analysis
Feature
Database
Documentation
Ontology
Web-based
Network2Canvas
BD2K-LINCS DCIC
Network visualization on a canvas with enrichment analysis
Data Type
Transcript Data
Role
Data Analysis
Data Formatting
Data Integration
Data Visualization
Network Analysis
Signature Generation
Feature
Documentation
Open Source
Search Engine
Versioning
Web-based
LINCS Canvas Browser
BD2K-LINCS DCIC
LCB provides interactive clustering with enrichment of L1000 signatures
Data Type
Protein Data
Role
Data Visualization
Network Analysis
Feature
Database
Search Engine
Web-based
cynetworkbrowser
BD2K-LINCS DCIC
An interactive tool for generating and viewing protein interaction networks
Data Type
Transcript Data
Role
Data Analysis
Data Documentation
Data Visualization
Network Analysis
Feature
Search Engine
Web-based
Touchstone App
LINCS Transcriptomics
Collection of CMap reference signatures
Data Type
Protein Data
Role
Data Visualization
Feature
Documentation
Open Source
Provenance
Web-based
Cell Dynamics Browser
HMS LINCS
Online tool for live-cell image data visualization
Data Type
Cell State Data
Drug Binding Data
Protein Data
Transcript Data
Role
Data Analysis
Data Integration
Data Visualization
Network Analysis
Signature Generation
Feature
API
Command Line
Database
Documentation
Open Source
Web-based
eXpression2Kinases
BD2K-LINCS DCIC
Linking expression signatures to upstream cell signaling networks
Data Type
Transcript Data
Role
Data Analysis
Data Formatting
Data Integration
Data Storage
Data Visualization
Signature Generation
Feature
API
Database
Search Engine
Versioning
Web-based
Slicr
BD2K-LINCS DCIC
A metadata search engine that provides easy access to L1000 GEO data
Data Type
Cell State Data
Protein Data
Transcript Data
Role
Data Analysis
Data Integration
Data Visualization
Network Analysis
Feature
API
Database
Documentation
Search Engine
Web-based
AChroMap
NeuroLINCS
A data integration tool for transcriptomic and epigenomic data
Data Type
Transcript Data
Role
Data Analysis
Data Documentation
slinky
R package to query the L1000 metadata via the CLUE.io REST API
Data Type
Transcript Data
Role
Data Analysis
Data Integration
Data Visualization
Network Analysis
Signature Generation
Feature
API
Database
Documentation
Ontology
Search Engine
Web-based
GEN3VA
BD2K-LINCS DCIC
Aggregates and analyzes gene expression signatures extracted from GEO
Data Type
Cell State Data
Role
Data Analysis
Data Formatting
Data Integration
Data Visualization
Signature Generation
Feature
Documentation
Open Source
Provenance
Scripting
Web-based
GR Browser
HMS LINCS
BD2K-LINCS DCIC
Online tool for calculating dose-response metrics and browsing response data
Data Type
Cell State Data
Drug Binding Data
Morphology Data
Protein Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Network Analysis
Signature Generation
Feature
Database
Documentation
Provenance
Search Engine
Versioning
Web-based
DToxS Portal
DToxS
Web portal to provide access to the DToxS Center's data, metadata and analyses
Data Type
Cell State Data
Morphology Data
Protein Data
Transcript Data
Role
Data Documentation
Data Formatting
Data Storage
Feature
Documentation
Open Source
Provenance
ImageRail
HMS LINCS
Desktop software for formatting and analyzing high-throughput image data
Data Type
Cell State Data
Morphology Data
Role
Data Analysis
Data Integration
Data Visualization
Signature Generation
Feature
Search Engine
Web-based
MEPmosaic
BD2K-LINCS DCIC
Mosaic visualization of high-content imaging assays of three cancer cell types
Data Type
Transcript Data
Role
Data Analysis
Data Integration
Data Storage
Data Visualization
Network Analysis
Signature Generation
Feature
API
Command Line
Database
Open Source
Scripting
Search Engine
Web-based
ARCHS4
BD2K-LINCS DCIC
Massive mining of publicly available RNA-seq data from human and mouse
Data Type
Cell State Data
Protein Data
Role
Data Visualization
Signature Generation
Feature
Documentation
Open Source
Provenance
Web-based
GF Response Browser
HMS LINCS
Online tool for browsing growth factor-stimulated cell signaling profiles
Data Type
Protein Data
Role
Data Analysis
Data Integration
Network Analysis
Feature
Web-based
PIUMet
NeuroLINCS
Tool for discovering pathways of peaks from untargeted metabolomics data
Data Type
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Network Analysis
Signature Generation
Feature
API
Database
Open Source
Search Engine
Web-based
BioJupies
BD2K-LINCS DCIC
Automatically generates RNA-seq data analysis notebooks
Data Type
Protein Data
Role
Data Integration
Data Visualization
Network Analysis
Signature Generation
Feature
Documentation
Open Source
Provenance
Web-based
Adaptation Browser
HMS LINCS
Online tool for browsing melanoma cell line adaptive resistance mechanisms
Data Type
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Visualization
Feature
Database
Web-based
Morpheus App
LINCS Transcriptomics
An interactive version of the ICV that lets you manipulate and annotate an existing dataset
Data Type
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Visualization
Feature
Database
Search Engine
Web-based
ICV App
LINCS Transcriptomics
A matrix-based interactive heatmap to explore relationships within the data
Data Type
Transcript Data
Role
Data Analysis
Data Visualization
GREIN
BD2K-LINCS DCIC
Interactive web platform for re-analyzing GEO RNA-seq data
Data Type
Protein Data
Transcript Data
Role
Data Analysis
Data Integration
Data Visualization
Network Analysis
Feature
Documentation
Web-based
PAEA
BD2K-LINCS DCIC
Enrichment analysis tool implementing the principal angle method
Data Type
Protein Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Network Analysis
Feature
Database
Documentation
Search Engine
Versioning
Web-based
Phosphosite Plus
BD2K-LINCS DCIC
Comprehensive resource for the study of protein post-translational modifications
Data Type
Cell State Data
Drug Binding Data
Protein Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Visualization
Network Analysis
Signature Generation
Feature
API
Database
Open Source
Search Engine
Web-based
Datasets2Tools
BD2K-LINCS DCIC
A platform for the discovery and evaluation of biomedical digital objects
Data Type
Protein Data
Role
Data Analysis
Data Formatting
Data Storage
Data Visualization
Signature Generation
Feature
API
Database
Search Engine
Versioning
Web-based
piLINCS
BD2K-LINCS DCIC
Provides interface and access to LINCS proteomics datasets available in Panorama
Data Type
Cell State Data
Morphology Data
Protein Data
Transcript Data
Role
Data Documentation
Data Formatting
Data Storage
Data Visualization
Feature
API
Database
Documentation
Ontology
Open Source
Provenance
Search Engine
Web-based
OMERO
HMS LINCS
Client-server software for image data visualization, management, and analysis
Data Type
Cell State Data
Morphology Data
Role
Data Analysis
Data Documentation
Data Storage
Data Visualization
Feature
API
Database
Search Engine
Web-based
clarion
MEP LINCS
Millions of microenviroment perturbations at a click
Data Type
Protein Data
Role
Data Visualization
Signature Generation
Feature
Documentation
Open Source
Provenance
Web-based
RTK Profile Browser
HMS LINCS
Online tool for browsing breast cancer cell line RTK profiles
Feature
Documentation
Web-based
GUIdock
BD2K-LINCS DCIC
Docker package containing a computational environment to run apps with a GUI
Data Type
Protein Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Signature Generation
Feature
API
Database
Documentation
Open Source
Search Engine
Web-based
Panorama
LINCS PCCSE
Proteomics repository that provides access to the PCCSE P100 and GCP data
Data Type
Cell State Data
Drug Binding Data
Morphology Data
Protein Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Network Analysis
Signature Generation
Feature
API
Command Line
Database
Documentation
Ontology
Open Source
Provenance
Scripting
Search Engine
Versioning
Web-based
LINCS Project Mobile
BD2K-LINCS DCIC
A mobile application to explore LINCS centers and resources
Data Type
Protein Data
Role
Data Analysis
Data Formatting
Data Integration
Feature
Web-based
PiNET
BD2K-LINCS DCIC
Used to annotate, map and analyze a set of peptide moieties
Data Type
Drug Binding Data
Role
Data Visualization
Network Analysis
Feature
Open Source
Web-based
LJP-BCNB
BD2K-LINCS DCIC
LINCS Joint Project-Breast Cancer Network Browser is an interactive viz of 2344 signatures
Data Type
Drug Binding Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Integration
Data Storage
Data Visualization
Feature
API
Database
Ontology
Open Source
Search Engine
Web-based
Drugmonizome
BD2K-LINCS DCIC
Search engine for querying annotated sets of drugs and small molecules
Data Type
Drug Binding Data
Protein Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Signature Generation
Feature
API
Database
Documentation
Ontology
Open Source
Search Engine
Web-based
DrugShot
BD2K-LINCS DCIC
Submit biomedical terms to receive ranked lists of relevant drugs and small molecules
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Visualization
Feature
Command Line
Documentation
Open Source
Scripting
blitzGSEA
BD2K-LINCS DCIC
Provides a computationally performant gene set enrichment analysis
Data Type
Cell State Data
Morphology Data
Protein Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Network Analysis
Signature Generation
Feature
Documentation
Open Source
Scripting
Web-based
Appyters
BD2K-LINCS DCIC
Collection of web-based applications to execute bioinformatics workflows
Data Type
Transcript Data
Role
Data Analysis
Data Documentation
Data Visualization
Network Analysis
Feature
Documentation
Ontology
Open Source
Search Engine
Web-based
Enrichr-KG
BD2K-LINCS DCIC
Integrates data from several gene-set libraries and presents gene-attribute associations
Data Type
Cell State Data
Protein Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Integration
Data Storage
Data Visualization
Feature
API
Documentation
Ontology
Open Source
Web-based
GeneShot
BD2K-LINCS DCIC
Submit biomedical terms to receive ranked lists of relevant genes
Data Type
Transcript Data
Role
Data Analysis
Data Integration
Feature
API
Documentation
Ontology
Open Source
Scripting
Search Engine
Web-based
PrismExp
BD2K-LINCS DCIC
Package for gene function predictions by unsupervised gene expression partitioning
Data Type
Transcript Data
Role
Data Analysis
Data Visualization
Feature
API
Database
Ontology
Open Source
Provenance
Scripting
Search Engine
Web-based
ChEA3
BD2K-LINCS DCIC
Predicts transcription factors (TFs) associated with user-input sets of genes
Data Type
Cell State Data
Morphology Data
Protein Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Network Analysis
Signature Generation
Feature
API
Command Line
Database
Ontology
Open Source
Search Engine
Web-based
X2K Web
BD2K-LINCS DCIC
Infers upstream regulatory networks from signatures of differentially expressed genes
Data Type
Cell State Data
Drug Binding Data
Morphology Data
Protein Data
Transcript Data
Role
Data Analysis
Data Formatting
Data Integration
Data Storage
Data Visualization
Signature Generation
Feature
Database
Documentation
Ontology
Open Source
Search Engine
Web-based
Structural Signature
DToxS
Identify protein features found in a gene or protein set
Data Type
Protein Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Feature
Database
Documentation
Ontology
Open Source
Provenance
Web-based
MFC10A
MEP LINCS
Dataset catalogs the transcriptional, proteomic, epigenomic and phenotypic changes experienced by MCF10A
Data Type
Cell State Data
Protein Data
Transcript Data
Role
Data Analysis
Data Integration
Data Storage
Data Visualization
Network Analysis
Feature
API
Database
Documentation
Open Source
Search Engine
Versioning
Web-based
KEA3
BD2K-LINCS DCIC
Infers upstream kinases whose putative substrates are overrepresented in a user-inputted list
Data Type
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Feature
Database
Documentation
Open Source
Web-based
Dex-Benchmark
BD2K-LINCS DCIC
Provides datasets and template workflows needed for benchmarking different tools for gene expression analysis
Data Type
Cell State Data
Drug Binding Data
Morphology Data
Protein Data
Transcript Data
Role
Data Analysis
Data Integration
Data Storage
Data Visualization
Signature Generation
Feature
API
Ontology
Open Source
Provenance
Scripting
Search Engine
Web-based
lncHUB2
BD2K-LINCS DCIC
Functional predictions of human lncRNAs based on lncRNA-gene co-expression correlations
Data Type
Protein Data
Transcript Data
Role
Data Analysis
Data Formatting
Data Integration
Data Visualization
Signature Generation
Feature
Documentation
Open Source
Scripting
Versioning
Web-based
Multiomics2Target
BD2K-LINCS DCIC
Discover cell surface and kinase targets for cohorts of cancer patients profiled with multi-omics
Data Type
Drug Binding Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Network Analysis
Feature
Database
Ontology
Open Source
Scripting
Search Engine
Web-based
Reprotox-KG
BD2K-LINCS DCIC
Provides a resource for exploring knowledge about the molecular mechanisms of birth defects
Data Type
Transcript Data
Role
Data Documentation
Data Formatting
Data Integration
Data Storage
Feature
API
Database
Documentation
Open Source
Scripting
Search Engine
Versioning
Web-based
RummaGEO
BD2K-LINCS DCIC
Enables gene expression signature search against the human and mouse RNA-seq studies deposited into GEO
Data Type
Drug Binding Data
Protein Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Network Analysis
Signature Generation
Feature
API
Database
Documentation
Ontology
Open Source
Scripting
Search Engine
Versioning
Web-based
Data Distillery KG
BD2K-LINCS DCIC
KG database represents interrelated biomedical ontologies and vocabularies
Data Type
Cell State Data
Drug Binding Data
Morphology Data
Protein Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Visualization
Network Analysis
Signature Generation
Feature
API
Documentation
Open Source
Scripting
Search Engine
Versioning
Web-based
Playbook Workflow
BD2K-LINCS DCIC
Web-based platform to construct biomedical workflows
Data Type
Drug Binding Data
Protein Data
Transcript Data
Role
Data Documentation
Data Formatting
Data Integration
Data Storage
Signature Generation
Feature
API
Database
Documentation
Open Source
Scripting
Search Engine
Versioning
Web-based
Rummagene
BD2K-LINCS DCIC
Web server application provides access to gene sets extracted from supporting materials of PMC publications
Data Type
Drug Binding Data
Protein Data
Transcript Data
Role
Data Analysis
Data Documentation
Data Formatting
Data Integration
Data Storage
Data Visualization
Network Analysis
Signature Generation
Feature
Database
Documentation
Ontology
Open Source
Scripting
Search Engine
Versioning
Web-based
CFDE GSE
BD2K-LINCS DCIC
Provides gene set libraries created from CF program datasets to serve an integrated cross-program enrichment analysis