Please suggest tools, API's/libraries to reverse engineer Gene regulatory networks from transcriptiomic data sets ( microarray / deep sequencing).
Thank you.
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written
by
Pradeep •
3 answers
Here is a list of references, both primary literature and reviews, organized by DREAM. DREAM is a yearly challenge for reverse engineering methods modeled after a similar competition for protein structure prediction. The basic approaches (Mutual Information, Bayesian Networks, Correlation, etc) are represented. Andrea Califano's group at Columbia has been prolific in this area with their ARACHNE algorithm.
check out this paper[?] Bioinformatics applications for pathway analysis of microarray data
Here is a shameless plug for AIRnet, a piece of software written by a former colleague and friend of mine.
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Weighted gene regulatory networks
written by hkarakurt
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Difference between Gene co-expression network and Gene regulatory network
written by Mike
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How to identify significant differentially expressed genes and gene regulatory networks from microa…
written by morteza.mahmoudisaber
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Is microarray gene expression analysis is dead ?
written by cjgunase •
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Genetic regulatory networks analysis for deep RNA seq data
written by hana
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Gene Regulatory Network using micro array data
written by mohammad.shaheryar •
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Methodology And Tools ( Python, Java Or R) For Drug-Target-Fishing
written by Pradeep •
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R Or Python Package For Reverse/Inverse Docking ( To Use A Ligand To Fish All The Targets)
written by Pradeep •
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Parsing Obo File
written by pradeep •
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Publications To Understand Statistics That Could Be Used For Finding Over And Under Represented Ter…
written by Pradeep •
