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

页数：5

共 50 条

[11] The DynaSig-ML Python']Python package: automated learning of biomolecular dynamics-function relationships
Mailhot, Olivier
Major, Francois
Najmanovich, Rafael
BIOINFORMATICS, 2023, 39 (04)
[12] FinTDA: Python']Python package for estimating market change through persistent homology diagrams
Souto, Hugo Gobato
Baris, Ismail
Heuvel, Storm Koert
Moradi, Amir
SOFTWARE IMPACTS, 2024, 20
[13] SurvLIMEpy: A Python']Python package implementing SurvLIME
Pachon-Garcia, Cristian
Hernandez-Perez, Carlos
Delicado, Pedro
Vilaplana, Veronica
EXPERT SYSTEMS WITH APPLICATIONS, 2024, 237
[14] Applications of python']python package for statistical engineering
Jang, Dae-Heung
KOREAN JOURNAL OF APPLIED STATISTICS, 2021, 34 (04) : 633 - 658
[15] A Python']Python package for particle physics analyses
Bevan, Adrian
Charman, Thomas
Hays, Jonathan
23RD INTERNATIONAL CONFERENCE ON COMPUTING IN HIGH ENERGY AND NUCLEAR PHYSICS (CHEP 2018), 2019, 214
[16] tension: A Python']Python package for FORCE learning
Liu, Lu Bin
Losonczy, Attila
Liao, Zhenrui
PLOS COMPUTATIONAL BIOLOGY, 2022, 18 (12)
[17] danRerLib: a Python']Python package for zebrafish transcriptomics
Schwartz, Ashley, V
Sant, Karilyn E.
George, Uduak Z.
BIOINFORMATICS ADVANCES, 2024, 4 (01):
[18] litstudy: A Python']Python package for literature reviews
Heldens, Stijn
Sclocco, Alessio
Dreuning, Henk
van Werkhoven, Ben
Hijma, Pieter
Maassen, Jason
van Nieuwpoort, Rob V.
SOFTWAREX, 2022, 20
[19] MGtoolkit: A python']python package for implementing metagraphs
Ranathunga, D.
Nguyen, H.
Roughan, M.
SOFTWAREX, 2017, 6 : 91 - 93
[20] celmech: A Python']Python Package for Celestial Mechanics
Hadden, Sam
Tamayo, Daniel
ASTRONOMICAL JOURNAL, 2022, 164 (05):

← 1 2 3 4 5 →