User: mhasa006

gravatar for mhasa006
mhasa00630
Reputation:
30
Status:
New User
Location:
United States
Last seen:
2 days, 13 hours ago
Joined:
3 years, 2 months ago
Email:
m*******@ucr.edu

Posts by mhasa006

<prev • 19 results • page 1 of 2 • next >
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Extract the SAM File header section
... How can I extract the header section of the SAM File with `htsjdk` package? Below is an example of a SAM File @HD VN:1.3 SO:coordinate @SQ SN:chr1 LN:248956422 @SQ SN:chr10 LN:133797422 @SQ SN:chr11 LN:135086622 XXX:111:312:1312 99 chr1 ...
htsjdk java bam samtools sam written 6 days ago by mhasa00630 • updated 5 days ago by Pierre Lindenbaum110k
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Forum: Cancer related problem with sequencing data and deep neural network
... I am fairly new to both Cancer research and Deep Neural Networks (DNN). I want to do some research mostly classification problem using the sequence data in the area of cancer research. Could anyone guide me towards the materials/publications I can read regarding this? I have tried to do cancer type ...
forum sequence rna-seq deep neural network cancer written 3 months ago by mhasa00630
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OG/Fusion, TSG/Fusion in CGC
... In Cancer Gene Census (CGC) dataset, ([cgc link][1], there is a column named Role in cancer. The values of this attributes are 'fusion', 'oncogene', 'oncogene, fusion', 'oncogene, TSG', 'TSG, fusion', 'oncogene, TSG'. What does the 'fusion' mean? Does this mean a mixture? Or a gene that sometimes ac ...
tsg cgc og cancer written 5 months ago by mhasa00630 • updated 5 months ago by Sean Davis24k
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Comment: C: Cancer research for computer science student
... Thanks for the good wishes. And it's he :-) ...
written 8 months ago by mhasa00630
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5 follow
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Forum: Cancer research for computer science student
... Hello, I am a Ph.D. student in Computer Science. My research interest is in computational biology. I have finished a project on epigenetics and now I want to work on Cancer genetic. I am particularly interested in cancer research but I don't have much of an experience with it. My advisor does not wo ...
bioinformatics computer science forum research cancer written 8 months ago by mhasa00630 • updated 8 months ago by Michael Dondrup44k
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Comment: C: Where To Find A Good Estimate Of The Background Mutation Rate In Rattus Norvegic
... This is probably a very long shot to get an answer. Still, asking... Could you please describe how the "Estimated Background mutation frequencies per million bp" table in the supplementary document was calculated? Is it purely experimental? Is it possible to compute the table by us? @Bioinfosm ...
written 9 months ago by mhasa00630
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Comment: C: RSEM output file format
... Thank you very much! I apologize for not being clear enough about the question, but your answer actually answered my question. ...
written 9 months ago by mhasa00630
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RSEM output file format
... I followed the following tutorial for RNA-Seq data analysis. https://ycl6.gitbooks.io/rna-seq-data-analysis/ After performing the Differential expression analysis using R (https://ycl6.gitbooks.io/rna-seq-data-analysis/perform_de_analysis.html) the final output files are `DE_analysis.gene.txt` and ...
rsem rna-seq differential expression written 10 months ago by mhasa00630 • updated 9 months ago by Jake Warner640
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Comment: C: Dataset preparation for driver/passenger gene discovery
... Thank you very much for your detailed reply. I'll read these links and ask a further question if any. ...
written 10 months ago by mhasa00630
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Dataset preparation for driver/passenger gene discovery
... I want to work on a project to find driver/passenger genes in cancer dataset. I want to build a statistical model by analyzing various types of data such as copy number variation, gene expression, methylation, somatic point mutations etc. on TCGA datasets like BRCA. Can someone explain the preproces ...
gene tcga snv snp cancer written 10 months ago by mhasa00630 • updated 10 months ago by Kevin Blighe24k

Latest awards to mhasa006

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Extract gff of a particular chromosome
Popular Question 5 months ago, created a question with more than 1,000 views. For Pulse information of PacBio data
Popular Question 8 months ago, created a question with more than 1,000 views. For Pulse information of PacBio data
Popular Question 24 months ago, created a question with more than 1,000 views. For Pulse information of PacBio data
Popular Question 24 months ago, created a question with more than 1,000 views. For PacBio data assembly with Celera

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