User: nazaninhoseinkhan

Reputation:
380
Status:
Trusted
Location:
Iran, Islamic Republic Of
Last seen:
1 week, 4 days ago
Joined:
6 years 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 • 271 results • page 1 of 28 • next >
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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 4 weeks ago by nazaninhoseinkhan380
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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 4 weeks ago by nazaninhoseinkhan380
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Problem in matching "days_to_last_followup" to the sample IDs in TCGA clinical files
... Dear all, I want to specify followup samples for each individual patients in TCGA data. However TCGA sample IDs are unique and I don't know how I can find samples belong to the same patient. Can you guide my how I can do this task? I appreciate any help Nazanin ...
tcga clinical file written 4 weeks ago by nazaninhoseinkhan380
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How to make a representative copy number variation sample from several samples based on their overlaps?
... Dear all, I want to compare copy number variations between a tumor and its corresponding normal samples for all my tumor samples. I am working on TCGA data and unfortunately all tumor samples have not their corresponding normal samples. I want to make a representative copy number variation sample ...
copy number variations getting overlaps written 5 weeks ago by nazaninhoseinkhan380 • updated 5 weeks ago by jared.andrews074.1k
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Unable to find normal samples in TCGA Esoghagus cancer samples
... Dear all, I want to identify normal (non-tumorous) samples in TCGA data of Esophagus cancer. I checked the submitter IDs of clinical data to inspect the forth part of TCGA data which shows if the sample belongs to tumor tissue (-01A) or normal tissue (- 11A), however the corresponding TCGA codes o ...
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Comment: C: how to get copy number alteration results for each patients?
... Thank you so much Kevin! Our team is in debt to you for all your helps ...
written 7 weeks ago by nazaninhoseinkhan380
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Comment: C: how to get copy number alteration results for each patients?
... Thanks Kevin, Just for clarification, I have to use findOverlaps()? ...
written 7 weeks ago by nazaninhoseinkhan380
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Comment: C: how to get copy number alteration results for each patients?
... Hi, Kevin, You mean I can generate a representative normal sample using GenomicRanges and then compare it with each individual tumor sample of my interest? ...
written 7 weeks ago by nazaninhoseinkhan380
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Comment: C: how to get copy number alteration results for each patients?
... Hi Kevin! If I understand correctly, if I want to compare segment means in each individual sample, I need to have pairs of tumor and normal samples. However as you know the number of normal samples are very small compared to tumor samples and therefore I do not have pairs of tumor and normal sampl ...
written 7 weeks ago by nazaninhoseinkhan380
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Comment: C: how to get copy number alteration results for each patients?
... Hi Kevin! I have around 100 patients without any mutations and I wanted to see what is the pattern of their copy number alterations and methylations. Would it be correct if I consider the segment_mean value and B value columns of those patients? Or I need to do some preprocessing? Nazanin ...
written 7 weeks ago by nazaninhoseinkhan380

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For Downloading data from TCGA
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Popular Question 6 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
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Popular Question 10 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 Difficulty in getting GTF file from iGenomes

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