Moderator: Friederike

gravatar for Friederike
Friederike5.2k
Reputation:
5,160
Status:
Trusted
Location:
United States
Last seen:
3 days, 8 hours ago
Joined:
4 years, 8 months ago
Email:
f******@med.cornell.edu

Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

http://abc.med.cornell.edu/

Posts by Friederike

<prev • 623 results • page 1 of 63 • next >
2
votes
1
answer
90
views
1
answers
Answer: A: computeMatrix bed format files
... A BED file is a simple tab-separated text file where the first three columns contain the chromosome, start and end position of a specific region of interest. There's a snippet shown in the [deepTools documentation](https://deeptools.readthedocs.io/en/latest/content/help_glossary.html#bed), too. As ...
written 11 days ago by Friederike5.2k
0
votes
6
answers
894
views
6
answers
Comment: C: Single Cell RNA Seq. Analysis
... I also want to point out the truly excellent write-up of numerous people involved in the development of the infrastructure for analyzing scRNA-seq using R packages hosted on bioconductor: ["Orchestrating single-cell analysis"](https://osca.bioconductor.org/) ...
written 23 days ago by Friederike5.2k
0
votes
2
answers
200
views
2
answers
Comment: C: Pull number of cells in cluster from seurat object
... I usually assign the content of the metadata to a separate object, which tends to make subsequent manipulations easier. I am a fan of the [data.table](https://www.listendata.com/2016/10/r-data-table.html) package, but I'm sure there are solutions using the [tidyverse/dplyr](https://dplyr.tidyverse. ...
written 4 weeks ago by Friederike5.2k
0
votes
1
answer
109
views
1
answers
Comment: C: What is the difference between tissues and cell lines in ENCODE>
... If the origin of the cells is of great importance, you'll definitely have to double check with the actual lab that generated the data. ENCODE is the parent organization for numerous individual labs/grants, and some specialized assays, e.g. ATAC-seq, may be performed on different types of, say, liver ...
written 4 weeks ago by Friederike5.2k
1
vote
1
answer
109
views
1
answers
Answer: C: What is the difference between tissues and cell lines in ENCODE>
... Cell lines are usually derived from cancerous cells. The ENCODE samples from tissues represent tissues taken from deceased donors (in the case of human data) or wildtype Bl6 mice. I.e. the tissues are probably as close to "healthy" or "normal" tissue as you can get. ...
written 5 weeks ago by Friederike5.2k
1
vote
1
answer
109
views
1
answers
Comment: C: What is the difference between tissues and cell lines in ENCODE>
... That'll depend on the overall goal of your analysis. For example, if you would like to compare the ENCODE results with some results you or a collaborator have obtained from, say, K562 cells, then it would probably make sense to download those. ...
written 5 weeks ago by Friederike5.2k
1
vote
0
answers
166
views
0
answers
Comment: C: How to add significant cut off in manhattan plot
... How exactly do you envision it to be added? Just as a number printed on the plot? Or via a line/asterisk/....? ...
written 5 weeks ago by Friederike5.2k
1
vote
2
answers
224
views
2
answers
Comment: C: How I know a file is sam or bam, sorted or unsorted
... So it was a problem with the memory. It'd be great if you could accept the answer that suggested that so that other users in the future will be pointed to the right track immediately. ...
written 5 weeks ago by Friederike5.2k
0
votes
1
answer
112
views
1
answers
Comment: C: convert VCF to gVCF
... >My goal is to extract all SNPs, not just the variations from reference. What do you mean by that? How were the SNPs determined in the first place if not by comparing your sequencing results to the reference genome? ...
written 5 weeks ago by Friederike5.2k
0
votes
1
answer
207
views
1
answers
Comment: C: R error: vector memory exhausted
... Don't you want `#NA / all` <= 0.05 then? ...
written 5 weeks ago by Friederike5.2k

Latest awards to Friederike

Scholar 11 days ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Good Answer 23 days ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Scholar 3 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Scholar 5 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Scholar 5 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Scholar 5 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Scholar 5 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1337 users visited in the last hour