PathCORE specifications

Information


Unique identifier OMICS_19033
Name PathCORE
Interface Web user interface
Restrictions to use None
Input data A weight matrix, a gene signature definition and a list of pathway definitions.
Input format TSV
Output data A graphic with pathway-pathway connections from global gene expression patterns.
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Casey Greene <>

Additional information


https://pathcore-demo.herokuapp.com/ Demo: https://github.com/kathyxchen/PathCORE-demo

Information


Unique identifier OMICS_19033
Name PathCORE
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A table.
Input format TSV
Output data A graphic.
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Casey Greene <>

Additional information


https://pathcore-demo.herokuapp.com/ Demo: https://github.com/kathyxchen/PathCORE-demo

Publication for PathCORE

PathCORE in publications

 (8)
PMCID: 5940864
PMID: 29739993
DOI: 10.1038/s41598-018-24876-0

[…] sections from 92 post-nat lumpectomy specimens were scanned at 20x magnification (0.5 μm/pixel). the whole slide images (wsis) were annotated by an expert pathologist using the sedeen viewer (pathcore, toronto, canada). a total of n = 166 rectangular regions of interest (rois) were defined on the 92 wsis and, within these rois, the centers of nuclei figures were labeled as either […]

PMCID: 5869966
PMID: 29619278
DOI: 10.4103/jpi.jpi_1_18

[…] 2017 pathology visions conference. over the course of several days, three acquisition devices (leica-aperio, philips, and roche-ventana), one picture archiving and communication system image server (pathcore) and two viewers (pathcore and aidpath) revealed the use of their systems to communicate dicom whole slide images exported from the aforementioned scanners to a server, and thence […]

PMCID: 5758516
PMID: 29311558
DOI: 10.1038/s41598-017-18310-0

[…] for inspirata inc and also sits on its scientific advisory board. additionally his technology has been licensed to elucid bioimaging and inspirata inc. he is also involved in a nih u24 grant with pathcore inc., and an nih r01 grant with inspirata inc. his work is also partially sponsored by philips […]

PMCID: 5537609
PMID: 28368414
DOI: 10.1038/onc.2016.500

[…] and use committee at the university of illinois at chicago. patient slides and information were obtained from fully consenting patients in a de-identified manner from the northwestern university pathcore following local irb approval., this work is dedicated to the memory of our friend daniel wang, who recently lost his long and courageous fight with cancer. we appreciate the contributions […]


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PathCORE institution(s)
Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, Germany; Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, Germany
PathCORE funding source(s)
KMC was funded by an undergraduate research grant from the Penn Institute for Biomedical Informatics; Gordon and Betty Moore Foundation (GBMF 4552) and Cystic Fibrosis Foundation (STANTO15R0); R01-AI091702.

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