Extracting interaction from RECON2 .mat file · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Extracting interaction from RECON2 .mat file

Hi,

I'm trying to extract the metabolic reactions and interactions from recon. I'm interested in just the network of interactions. I have been trying to find a way to extract the information from the matlab(.mat) file provided. I'm however unfamiliar with matlab and am unable to extract the metabolic network. I will be grateful for any points and help on how I can extract the relevant interactions from the matlab file.

Thanking You, Vakul

recon metabolic networks matlab

• 2,039 views • link

written 10.4 years ago by vakul.mohanty

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Automate the removal of cofactors from many reactions
written 7.1 years ago by davidtmscott

When constructing a metabolic network from a large number of reactions, is there a computational way to remove cofactors from the reactions. This also must …
PSCBS segmentation file header
written 9.3 years ago by vakul.mohanty

Hello, I'm have used Paired parent specific circular binary segmentation (PSCBS) to segment copy number calls made from SNP6 data and obtain copy numbers as …
Accounting for hidden batch effects in differential expression analysis with DEXseq and Slueth
written 9.4 years ago by vakul.mohanty

Hello, I'm looking to carry out DEXseq (for differential exon usage) and Slueth (differential gene expression) analysis on some TCGA BAM files. As the BAM …
Extract all the information of a pathway from a Biopax lv2 or 3 file
written 9.7 years ago by bergk_pinto •

Hi, I'm working on bacterial sulfur metabolism and I would like to be able to extract as much information as I can from the different …
Where can I find CCLE RNAseq BAM files?
written 9.9 years ago by vakul.mohanty

Hello, I'm trying to find where the raw sequencing data from CCLE was relocated after cghub was decommissioned, any pointers will be really helpful. Thanking …
eQTL analysis on TCGA RNAseq data and SNP6 data
written 10.2 years ago by vakul.mohanty

Hi, I'm trying to carry out eQTL analysis using genotype calls from SNP6 array(calls made using CRLMM) and expression from RNAseq from TCGA. I carried …
Retrieve all reactions for a given kegg pathway
written 10.3 years ago by neha 114 •

Hello, I am trying to derive all the reactions specific for a kegg pathway. For example " for metabolic pathway" from ehi :ehi01100 , I …
Is it correct to merge TCGA mutation data from multiple centers
written 10.6 years ago by vakul.mohanty

Hello, I recently started working with TCGA protected mutation data. The SNP calls provided are made across several centers using different sequencing protocols and SNP …
Error with cn.MOPS run on exomeseq data
written 10.7 years ago by vakul.mohanty

Hello, I'm having trouble with cn.MOPS. I run the following piece of code and receive an error library(cn.mops) bam = list.files(path = "/home/trantor/mounts/komurov_lab/SKCM_WES",pattern=".bam$",full.names=TRUE) seg = …
Draw metabolic map from matlab file
written 10.8 years ago by nhungptt17 •

Hi all, I have a metabolic model making from matlab. Now I'm looking for a tool to help me draw metabolic map from that matlab …