User: JJ

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JJ460
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Posts by JJ

<prev • 151 results • page 1 of 16 • next >
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Comment: C: TCGA CNV data - immensely different results depending on data source
... Thanks for your input!! > From what I understand, the data on the GDC itself (which TCGAbiolinks > uses) is just the segmented calls that have been called via Circular > Binary Segmentation. Try to think of it as a pseudo-raw form of copy > number (technically, it is just that because t ...
written 27 days ago by JJ460
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TCGA CNV data - immensely different results depending on data source
... Dear all, I am looking into genes of interest affected by CNVs using TCGA data. I am very confused about the immensely different results I get depending on the data source I use: The GDC data portal (also available via TCGAbiolinks R package) provides a simple data.frame (genes / patients with -1 ...
genome tcga cnv written 27 days ago by JJ460
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Comment: C: Pathway analysis with co-variates for RNA-seq data
... will do - thanks so much! ...
written 6 months ago by JJ460
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Comment: C: Pathway analysis with co-variates for RNA-seq data
... thanks so much for this pointer! ...
written 6 months ago by JJ460
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Pathway analysis with co-variates for RNA-seq data
... Hi all, I was wondering if someone knows of a tool to perform a pathway analysis with co-variates for RNA-seq data. What I mean in more detail is the following: I have two groups (cond. 1 vs. cond. 2) but I also have co-variates which will have an high impact on the expression (20-30 samples in t ...
rna-seq written 6 months ago by JJ460 • updated 6 months ago by Kevin Blighe48k
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Help with Designing an Approach for Biomarker Signature Generation
... Hi all, I am trying to design an experiment and could use some input. My goal is to generate a predictive gene signature, which can separate two groups BUT I have a number of confounding variables. My starting point are RNA-seq experiments. - compute gene expression from RNA-seq experiments (low ...
gene rna-seq written 6 months ago by JJ460
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Comment: C: SRA and the relationship between biosamples, experiments and runs
... Hi, thank you for taking another look! they are technical according to the [paper][1]. Thanks!!! [1]: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126911 ...
written 6 months ago by JJ460
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Comment: C: SRA and the relationship between biosamples, experiments and runs
... Thank you very much for your answer. However, I am still not getting it. Sorry ... I am trying to rap my head around it! > then before sequencing, the samples were prepared using 4 indexes, > that means the library preparation was done individually, generating > the 8 experiments. There ...
written 7 months ago by JJ460
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SRA and the relationship between biosamples, experiments and runs
... Dear all, Obviously I've read this (https://www.ddbj.nig.ac.jp/faq/en/biosample-bioproject-sra-e.html): > What is the relationship between BioSamples, SRA Experiments, SRA > Runs, and my data files? > > BioSample is descriptive information about > the biological source materials, ...
sequencing written 7 months ago by JJ460 • updated 7 months ago by JC8.4k
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Comment: C: Calculation of VAF (variant allele frequency)
... Thank you so much for your detailed answer! Now it's clear to me what the difference between MAF and VAF is and I am looking into the variant allele fraction and not MAF. I have a couple of cancer samples (actually cancer cell lines) and I want to look at the heterogeneity within each sample. I exp ...
written 7 months ago by JJ460

Latest awards to JJ

Popular Question 17 days ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 5 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 5 months ago, created a question with more than 1,000 views. For Is there a tool that sorts gtf files?
Popular Question 5 months ago, created a question with more than 1,000 views. For SNP calling using cancer cell lines
Popular Question 5 months ago, created a question with more than 1,000 views. For Public strand-specific RNA-seq data for human tissues
Popular Question 5 months ago, created a question with more than 1,000 views. For RSeQC Output from infer_experiment.py - what does it mean?
Popular Question 5 months ago, created a question with more than 1,000 views. For TCGA data - GDC data portal vs. Firebrowse
Popular Question 9 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Student 11 months ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Popular Question 12 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 12 months ago, created a question with more than 1,000 views. For Is there a tool that sorts gtf files?
Popular Question 12 months ago, created a question with more than 1,000 views. For Clustering data - data transformation (log2) highly improves clustering but why?
Voter 13 months ago, voted more than 100 times.
Popular Question 14 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 14 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Centurion 16 months ago, created 100 posts.
Student 16 months ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Scholar 16 months ago, created an answer that has been accepted. For A: Gene Expression data and variants from the same fastqc raw file
Supporter 22 months ago, voted at least 25 times.
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Help in writing NGS pipeline (or: the road from fasta to vcf)

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