User: atakanekiz

gravatar for atakanekiz
atakanekiz190
Reputation:
190
Status:
Trusted
Location:
Last seen:
2 hours ago
Joined:
1 year, 8 months ago
Email:
a*********@gmail.com

Posts by atakanekiz

<prev • 20 results • page 1 of 2 • next >
1
vote
1
answer
56
views
1
answers
Comment: C: Discrepancies in TCGAbiolinks subtype data
... Thanks for the insight. That was been my approach so far. Looking both places seems helpful for getting the best out of TCGA data. ...
written 2 days ago by atakanekiz190
0
votes
1
answer
56
views
1
answers
Comment: C: Discrepancies in TCGAbiolinks subtype data
... I prepared the SE object using query function via TCGAbiolinks as follows: query_harmonized_gene <- GDCquery(project = i, data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", ...
written 3 days ago by atakanekiz190
2
votes
1
answer
56
views
1
answer
Discrepancies in TCGAbiolinks subtype data
... Hello, I have a question regarding accessing the subtype information associated with TCGA projects using `TCGAbiolinks` package (in this example, specifically COAD but my question applies to other projects including SKCM for instance) When I download the RNAseq experiment as a SummarizedExperiment ...
tcgabiolinks tcga subtype summarizedexperiment written 3 days ago by atakanekiz190
0
votes
5
answers
9.3k
views
5
answers
Answer: A: GSEA analysis with Mouse (Please give some comments..)
... I tried GSEA with mouse data both by mapping the homologs using a proper method (ensembl/biomaRt as suggested here), and also by simply converting sentence case gene names (i.e. Pdcd1) to upper case (i.e. PDCD1). In my experience, these approaches work similarly. Using uppercase letters, for the mo ...
written 4 days ago by atakanekiz190
0
votes
0
answers
5.8k
views
0
answers
Comment: C: Survival analysis with gene expression
... Hi Kevin, Thank you very much for this helpful tutorial. I spent some time to figure out how to do this analysis before coming across your post. I'd appreciate if you can comment on my approach and please let me know if you find it inaccurate. I downloaded TCGA RNAseq and miRNAseq data and used `v ...
written 4 days ago by atakanekiz190
0
votes
0
answers
53
views
0
answers
Reading EMBL-like miRBase data into R
... Hello, I'm trying to use miRNA data from the [mirBase](http://www.mirbase.org/) database in some of my R pipelines. The data file I'm interested in is the [mirna.dat](http://www.mirbase.org/ftp.shtml) which contains info from all published miRNAs (across multiple species). One entry within the dat ...
R mirdb embl parse written 14 days ago by atakanekiz190
0
votes
2
answers
1.4k
views
2
answers
Comment: A: TCGA immunotherapy treated melanoma data
... This is an old post and I'm not sure if I'll get an answer on a related point, but here it goes... Is there a way of figuring out when the tumor samples were collected and when the immunotherapy started? I'm trying to understand if these patient samples are pre- or post-immunotherapy treatment. ...
written 3 months ago by atakanekiz190
0
votes
0
answers
1.6k
views
0
answers
Comment: C: Integrating VDJ sequencing data with Seurat
... Thanks for the suggestion. I was recycling that code snipped since early times of Seurat. I gotta keep up with times! ...
written 8 months ago by atakanekiz190
0
votes
1
answer
1.8k
views
1
answers
Answer: A: Associating VDJ clonotyping data with scRNA-seq in Seurat
... @j-andrews7 thanks for this vignette. I expanded it further to work with my own data. The detailed tutorial can be found at [my Biostars post](https://www.biostars.org/p/384640/). ...
written 8 months ago by atakanekiz190
8
votes
0
answers
1.6k
views
6 follow
0
answers
Tutorial: Integrating VDJ sequencing data with Seurat
... Jared.andrews07 wrote [a previous tutorial][1] for integrating TCR/VDJ sequencing data with Seurat object. I wanted to expand on this vignette to automate some data cleanup especially for Seurat objects created by combining more than one sequencing run. Unlike Jared's script, the method below will a ...
clonotyping vdj sc-rnaseq tutorial seurat written 8 months ago by atakanekiz190

Latest awards to atakanekiz

Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: TCGAbiolinks TCGA-BRCA RNA-seq clinical data
Popular Question 3 months ago, created a question with more than 1,000 views. For Integrating VDJ sequencing data with Seurat
Popular Question 7 months ago, created a question with more than 1,000 views. For Differences between RTCGA and TCGAbiolinks data
Student 7 months ago, asked a question with at least 3 up-votes. For Differences between RTCGA and TCGAbiolinks data
Appreciated 8 months ago, created a post with more than 5 votes. For Integrating VDJ sequencing data with Seurat
Scholar 19 months ago, created an answer that has been accepted. For A: Differences between RTCGA and TCGAbiolinks data
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: TCGAbiolinks TCGA-BRCA RNA-seq clinical data
Scholar 20 months ago, created an answer that has been accepted. For A: Differences between RTCGA and TCGAbiolinks data

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1207 users visited in the last hour