User: nazaninhoseinkhan

Reputation:
360
Status:
Trusted
Location:
Iran, Islamic Republic Of
Last seen:
3 days, 16 hours ago
Joined:
5 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 • 251 results • page 1 of 26 • next >
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Rarefaction curves does not show all sample curves
... Dear all, I am trying to get the rarefaction curves for my 15 metagenomics samples. However the resulted plot show me only 13 curves. Can you tell me the possible reasons for this? Is it possible that my low sequence number samples would have been removed from plot? Regards Nazanin ...
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Comment: C: Reading TCGA methylation .txt files in R
... Hi Kevin, Happy new year 2019. Wishing you a prosperous year. Thank you for your comment. I will merge the files as you suggest me and let you know the results ...
written 6 weeks ago by nazaninhoseinkhan360
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Reading TCGA methylation .txt files in R
... Dear all, I am trying to analyze Methylation data of cancer patients and compare them with normal samples. Since the size of methylation data was so huge, I decided to download the entire data as .tar.gz instead of using "GDCdownload" function available in TCGABiolinks. However I cannot find out ...
methylation analysis tcga written 6 weeks ago by nazaninhoseinkhan360
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Comment: C: error in introducing different batches to DeSeq2
... Dear all, I repeat the factor introduction steps and my problem was solved. Happy new year 2019 to all Galaxy members. I wish you all health, wealth and peace in 2019. Nazanin ...
written 7 weeks ago by nazaninhoseinkhan360
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(Closed) error in introducing different batches to DeSeq2
... Dear all, I faced with a problem in introducing different batches to DeSeq2. I have chemotherapy resistant ans sensitive samples that include 3 different cell line (1,2,3) and have been performed by 3 different illumina sequencer (HiSeq 2500, HiSeq 3000 and next seq). I got the htseq counts files ...
deseq2 introducing batches rna-seq written 7 weeks ago by nazaninhoseinkhan360
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Comment: C: Hierarchical clustering to group large number of samples
... Thanks for your comments. Sure. I will try dynamicTreeCut package ...
written 7 weeks ago by nazaninhoseinkhan360
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Hierarchical clustering to group large number of samples
... Dear all, I want to cluster around 250 normalized htseq count samples to get insight about how many distinct groups are present in my samples. I used hierarchical clustering using "Euclidean distance measure" available in GENE-E program. However I don't know is it OK if I select visually separat ...
sample clustering rna-seq written 7 weeks ago by nazaninhoseinkhan360 • updated 7 weeks ago by Jean-Karim Heriche18k
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Comment: C: Differential expression analysis on miRNA count files
... Thanks. My problem was solved a few weeks ago ...
written 7 weeks ago by nazaninhoseinkhan360
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Answer: A: Differential expression analysis on miRNA count files
... Hi, As I said in my post I do not know by which program this file has been generated. Some of my friends sent these files to me and asked me to do differential expression analysis on them. However the format of these files is not familiar. The files have are in bam format, however as you said it l ...
written 3 months ago by nazaninhoseinkhan360
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Differential expression analysis on miRNA count files
... Dear all, I want to perform differential expression analysis between two mirSeq samples. This is not my own project. I received bam files in the following format. However it is more similar to count file than alignment file: QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT @HD ...
mirseq differential expression written 3 months ago by nazaninhoseinkhan360 • updated 7 weeks ago by ahmad mousavi380

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Popular Question 27 days ago, created a question with more than 1,000 views. For Difficulty in getting GTF file from iGenomes
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Great Question 4 months ago, created a question with more than 5,000 views. For False discovery rate
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