Eliater: a Python']Python package for estimating outcomes of perturbations in biomolecular networks

被引：0
|
作者：
Mohammad-Taheri, Sara [1 ,2 ]
Navada, Pruthvi Prakash [2 ]
Hoyt, Charles Tapley [2 ]
Zucker, Jeremy [3 ]
Sachs, Karen [4 ,5 ]
Gyori, Benjamin M. [1 ,2 ,6 ]
Vitek, Olga [1 ,2 ]
机构：
[1] Northeastern Univ, Barnett Inst Chem & Biol Anal, Boston, MA 02115 USA
[2] Northeastern Univ, Khoury Coll Comp Sci, Boston, MA 02115 USA
[3] Pacific Northwest Natl Lab, Richland, WA 99354 USA
[4] Next Generat Analyt, Palo Alto, CA USA
[5] Modulo Bio Inc, Los Altos, CA 92121 USA
[6] Northeastern Univ, Dept Bioengn, Boston, MA 02115 USA
来源：
BIOINFORMATICS | 2024年 / 40卷 / 09期
关键词：
D O I：
10.1093/bioinformatics/btae527
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
We introduce Eliater, a Python package for estimating the effect of perturbation of an upstream molecule on a downstream molecule in a biomolecular network. The estimation takes as input a biomolecular network, observational biomolecular data, and a perturbation of interest, and outputs an estimated quantitative effect of the perturbation. We showcase the functionalities of Eliater in a case study of Escherichia coli transcriptional regulatory network. Availability and implementation The code, the documentation, and several case studies are available open source at https://github.com/y0-causal-inference/eliater.
引用
收藏
页数：5
相关论文
共 50 条
  • [21] Astropy: A community Python']Python package for astronomy
    Robitaille, Thomas P.
    Tollerud, Erik J.
    Greenfield, Perry
    Droettboom, Michael
    Bray, Erik
    Aldcroft, Tom
    Davis, Matt
    Ginsburg, Adam
    Price-Whelan, Adrian M.
    Kerzendorf, Wolfgang E.
    Conley, Alexander
    Crighton, Neil
    Barbary, Kyle
    Muna, Demitri
    Ferguson, Henry
    Grollier, Frederic
    Parikh, Madhura M.
    Nair, Prasanth H.
    Guenther, Hans M.
    Deil, Christoph
    Woillez, Julien
    Conseil, Simon
    Kramer, Roban
    Turner, James E. H.
    Singer, Leo
    Fox, Ryan
    Weaver, Benjamin A.
    Zabalza, Victor
    Edwards, Zachary I.
    Bostroem, K. Azalee
    Burke, D. J.
    Casey, Andrew R.
    Crawford, Steven M.
    Dencheva, Nadia
    Ely, Justin
    Jenness, Tim
    Labrie, Kathleen
    Lim, Pey Lian
    Pierfederici, Francesco
    Pontzen, Andrew
    Ptak, Andy
    Refsdal, Brian
    Servillat, Mathieu
    Streicher, Ole
    ASTRONOMY & ASTROPHYSICS, 2013, 558
  • [22] MeDIL: A Python']Python Package for Causal Modelling
    Markham, Alex
    Chivukula, Aditya
    Grosse-Wentrup, Moritz
    INTERNATIONAL CONFERENCE ON PROBABILISTIC GRAPHICAL MODELS, VOL 138, 2020, 138 : 621 - 624
  • [23] matplotlib - A portable python']python plotting package
    Barrett, P
    Hunter, J
    Miller, JT
    Hsu, JC
    Greenfield, P
    Astronomical Data Analysis Software and Systems XIV, Proceedings, 2005, 347 : 91 - 95
  • [24] The Multitaper Spectrum Analysis Package in Python']Python
    Prieto, German A.
    SEISMOLOGICAL RESEARCH LETTERS, 2022, 93 (03) : 1922 - 1929
  • [25] PYCHEM: a multivariate analysis package for python']python
    Jarvis, Roger M.
    Broadhurst, David
    Johnson, Helen
    O'Boyle, Noel M.
    Goodacre, Royston
    BIOINFORMATICS, 2006, 22 (20) : 2565 - 2566
  • [26] TDCRPy: A python']python package for TDCR measurements
    Coulon, Romain
    Hu, Jialin
    APPLIED RADIATION AND ISOTOPES, 2024, 214
  • [27] scqubits: a Python']Python package for superconducting qubits
    Groszkowski, Peter
    Koch, Jens
    QUANTUM, 2021, 5
  • [28] WavePy: A Python']Python Package for Wave Optics
    Beck, Jeffrey
    Bekins, Celina
    Bos, Jeremy P.
    LONG-RANGE IMAGING, 2016, 9846
  • [29] CosmoFlow: Python']Python package for cosmological correlators
    Werth, Denis
    Pinol, Lucas
    Renaux-Petel, Sebastien
    CLASSICAL AND QUANTUM GRAVITY, 2024, 41 (17)
  • [30] pyBSM: A Python']Python package for modeling imaging systems
    LeMaster, Daniel A.
    Eismann, Michael T.
    LONG-RANGE IMAGING II, 2017, 10204
12345