User: nazaninhoseinkhan

Reputation:
390
Status:
Trusted
Location:
Iran, Islamic Republic Of
Last seen:
2 days, 11 hours ago
Joined:
6 years, 2 months ago
Email:
n****************@gmail.com

I am Nazanin Hosseinkhan, PhD in Bioinformatics. My background is Microbiology and I am seeking for a postdoc position.

Posts by nazaninhoseinkhan

<prev • 279 results • page 1 of 28 • next >
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How to specify pipelines(muse, mutect,...) in TCGAbiolinks when you want to use hg19?
... Dear all, I am trying to use different mutation analysis pipelines(muse, mutect for my tumor samples using TCGABiolinks package. I want to use hg19 as the reference genome. However it seems that I can only specify the certain pipeline using "pipeline="muse" in "GDCquery_maf()" which is used when ...
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Comment: C: What should I do when some probes of a gene is detected as hypomethylated and ot
... I could find the annotation file from UCSC table browser ...
written 7 weeks ago by nazaninhoseinkhan390
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Comment: C: What should I do when some probes of a gene is detected as hypomethylated and ot
... Thanks Jan. Can u guide me how to find the probe annotation file for Illumina human methylation 450 array? ...
written 7 weeks ago by nazaninhoseinkhan390
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What should I do when some probes of a gene is detected as hypomethylated and other probes of the same gene is hypermethylated
... Dear all, I have carried out differential methylation analysis on TCGA data. Strangely I have found 13 genes detected as hypermethylated and hypomethylated at the same time. Different probes for the same genes show this discrepancy. My question is that should I remove these 13 genes from rest of ...
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problem in finding follow_up samples belong to the same patients in TCGA
... Dear all, I am trying to find the following up samples belong to the same patients in TCGA. I used TCGAbiolinks to get follow_up information, however neither TCGA follow up Id nor patients uuid's could be mapped to more than one sample. It seems they are unique. Can any body guide me how to get th ...
follow_up samples tcga codes written 10 weeks ago by nazaninhoseinkhan390
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Comment: C: No mutations or copy number alterations was detected in stage I of cancer
... Sure, thank u German ...
written 11 weeks ago by nazaninhoseinkhan390
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Comment: C: No mutations or copy number alterations was detected in stage I of cancer
... Thank you so much for the explanation ...
written 11 weeks ago by nazaninhoseinkhan390
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No mutations or copy number alterations was detected in stage I of cancer
... Dear all, I found no mutations or copy number alterations in about %30 of my tumor samples (stage one of tumor). Would you please tell me if it is strange? have anybody faced with the same issue? Regards Nazanin ...
stage one tumor snp copy number alteration written 11 weeks ago by nazaninhoseinkhan390
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Comment: C: how to get copy number alteration results for each patients?
... Hi Kevin! I made a representative normal sample based on the overlaps of regions among several normal samples. Now my questions is how can I compare the segment_mean values of each of my tumor samples with the segment_mean of the constructed normal sample? Should I compare segment_means manually? ...
written 3 months ago by nazaninhoseinkhan390
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Comment: A: Problem in matching "days_to_last_followup" to the sample IDs in TCGA clinical f
... Hi Kevin! From the column " days to last follow up" , I concluded that there are more than one sample for each patient and these samples have been gathered during following up of that patient. However I could not find out samples belong to same patient. How I can identify samples collected during ...
written 3 months ago by nazaninhoseinkhan390

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Popular Question 10 days ago, created a question with more than 1,000 views. For WGCNA module membership cutoff
Popular Question 10 days ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
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Popular Question 5 months ago, created a question with more than 1,000 views. For Difficulty in getting GTF file from iGenomes
Popular Question 5 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
Popular Question 5 months ago, created a question with more than 1,000 views. For Difficulty in getting GTF file from iGenomes
Popular Question 5 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
Popular Question 6 months ago, created a question with more than 1,000 views. For Difficulty in getting GTF file from iGenomes
Popular Question 6 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
Popular Question 6 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 9 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
Popular Question 9 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
Popular Question 9 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
Popular Question 11 months ago, created a question with more than 1,000 views. For WGCNA module membership cutoff
Popular Question 11 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 11 months ago, created a question with more than 1,000 views. For Difficulty in getting GTF file from iGenomes
Popular Question 11 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
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