User: modarzi

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modarzi10
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Posts by modarzi

<prev • 44 results • page 1 of 5 • next >
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Answer: A: Where To Look For Quality Bioinformatics Short Courses And Workshops?
... Hi, In coursera.org you can find Bioinformatics Specialization that is perfect sources for learning bioinformatic. based on below link you can find 7 courses under bioinformatic: https://www.coursera.org/specializations/bioinformatics#courses Best Regards, Mohammad ...
written 9 hours ago by modarzi10
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Comment: C: problem for comparing 2 type of annotation file
... Thanks, Dear Dr. Blighe Hi, As you know, my data set belong to TCGA and the labels of genes that I see in my downloaded file is e.g. same as ENSG00000000003. Again, in WGCNA, I have to provide annotation file same as WGCNA tutorial(GeneAnnotation.csv). based on that, I wrote an email to Dr. Lan ...
written 1 day ago by modarzi10
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Comment: C: problem for comparing 2 type of annotation file
... I mean that these 2 file have any structural different. because I couldn't [read][1] gencode.v22.annotation.gtf file via "refGenome" package.but I can read Homo_sapiens.GRCh38.92.gtf via refGenome package. So, I want to know can I use Homo_sapiens.GRCh38.92.gtf instead gencode.v22.annotation.gtf? I ...
written 3 days ago by modarzi10
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Comment: C: data pre-processing for WGCNA Algorithm
... Thanks, My data set is belong to TCGA. So, I found gencode.v22.annotation.gtf.gz as annotation file from below link: https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files Best Regards, Mohammad ...
written 3 days ago by modarzi10
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problem for comparing 2 type of annotation file
... Hi, For analyzing TCGA data set, I need annotation file. So, based on this link: https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files I downloaded gencode.v22.annotation.gtf but based on this link I couldn’t find read this file. So, my question is can I read Hom ...
tcga rna-seq gencode annotation file written 3 days ago by modarzi10
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Comment: C: data pre-processing for WGCNA Algorithm
... Thanks,now I have anothe problem. Dear Dr. Kevin Blighe I have another problem. As you know, in WGCNA tutorial is based on Microarray data set and my data set is RNA-seq expression. So I have to prepare annotation file same as Annotation.csv. Based on my data set, I downloaded gencode.v22.annotatio ...
written 3 days ago by modarzi10
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Comment: C: Error for reading .gtf file in R
... Thanks. I Download gff3 file from gencode (https://www.gencodegenes.org/releases/current.html) but I can't install gffread in R. > biocLite("gffread") BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23). Installing package(s) ...
written 3 days ago by modarzi10
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question for Accession No. : SSR
... I read this article: "Revelation of mRNAs and proteins in porcine milk exosomes by transcriptomic and proteomic analysis". So,in end of article and in the "Availability of data and materials" I saw that "All the RNA-Seq data for analysis in this study have been ​deposited in https://www.ncbi.nlm.n ...
ssr rna-seq written 4 days ago by modarzi10 • updated 4 days ago by ATpoint3.9k
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Comment: C: Error for reading .gtf file in R
... Thanks but "read.gtf in R" also was for me.anyway, can I use another version of annotation? for example latest version? or I have to use just that one? thanks from you if you share your comment with me. Best Regards, Mohammad ...
written 6 days ago by modarzi10
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Comment: C: Error for reading .gtf file in R
... Thanks but "read.gtf in R" also was for me.anyway, can I use another version of annotation? for example latest version? or I have to use just that one? thanks from you if you share your comment with me. Best Regards, Mohammad ...
written 6 days ago by modarzi10

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