Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller20k
Reputation:
20,230
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
Scholar ID:
Google Scholar Page
Last seen:
14 hours ago
Joined:
9 years ago
Email:
c***********@gmail.com

I work in the Division of Oncology and McDonnell Genome Institute at Washington University in St. Louis, where I develop and apply computational tools to give us insight into the origins and progression of cancer.

Posts by Chris Miller

<prev • 1,087 results • page 1 of 109 • next >
0
votes
1
answer
167
views
1
answers
Comment: C: CNVkit: Choice of Bin Size and CNV Calling
... CopyCat should work fine with newer R versions, as far as I know, and has a single-sample mode ...
written 25 days ago by Chris Miller20k
0
votes
1
answer
167
views
1
answers
Answer: A: CNVkit: Choice of Bin Size and CNV Calling
... It's a tradeoff. Larger bin sizes reduce noise, smaller bin sizes increase sensitivity. This figure (panels C and D) may offer some clarity on that point, as does some of the text immediately below https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016327#pone-0016327-g001 In gene ...
written 26 days ago by Chris Miller20k
1
vote
0
answers
249
views
0
answers
Job: Bioinformatics Developer/Analyst - Washington University in St. Louis
... Our cancer genomics team is expanding by adding additional analysts and developers. You'll join a well-established group of computationally-savvy researchers working on cutting edge questions in the field. This group, under the Genomics of AML Program Project Grant, sequenced the first human cancer ...
job wustl written 4 weeks ago by Chris Miller20k
0
votes
0
answers
1.3k
views
0
answers
Comment: C: Visualize VarScan2 Copy Number Aberrations in IGV
... The primary issue is that most copy number events are of size megabase or more. IGV works best on the base-to-kilobase scale. You certainly can make bed-like tracks that show your CN event, but it's probably not going to be the most helpful view.. ...
written 6 weeks ago by Chris Miller20k
3
votes
3
answers
299
views
3
answers
Answer: A: Reproducing this picture
... GenVisR is a good R package for this, as is ProteinPaint from St Jude: https://pecan.stjude.cloud/proteinpaint ...
written 6 weeks ago by Chris Miller20k
0
votes
1
answer
129
views
1
answers
Comment: C: Detecting known, low frequency SNPs in bacterial populations
... The output is specified in the readme here: https://github.com/genome/bam-readcount It gives you counts of each base at that position, along with some extra qc information (on quality, strand bias, etc) You will have to look at those numbers and formulate a way to set a minimum level of detection ...
written 7 weeks ago by Chris Miller20k
1
vote
1
answer
129
views
1
answers
Answer: A: Detecting known, low frequency SNPs in bacterial populations
... - As noted above, the parameters for varscan matter a lot. Relaxing them substantially will probably be helpful - If you have known positions, you can just use [bam-readcount](https://github.com/genome/bam-readcount) to query those directly, then apply whatever post-hoc filtering or statistics you ...
written 8 weeks ago by Chris Miller20k
1
vote
1
answer
251
views
1
answers
Answer: A: Does sciClone work on mouse exome data?
... I don't see why that wouldn't work, as long as there are enough somatic variants to track from the tumors. (Cluster confidence increases with number of variants and the depth of sequencing). ...
written 9 weeks ago by Chris Miller20k
0
votes
1
answer
173
views
1
answers
Answer: A: SciClone works with 1d clustering, but not 2d?
... Sorry that I missed this. You don't have your input vaf files formatted correctly. You have to actually merge your variant lists and get readcounts for each variant in all samples. (Not called is not the same as 0% vaf!) See this post (and several other under the sciclone tag) for more info. http ...
written 9 weeks ago by Chris Miller20k
1
vote
1
answer
165
views
1
answers
Answer: A: regions with very different VAF fall into one cluster
... You have not removed copy number altered variants from.your sample (this includes variants on sex Chris in males). Anything at 100% vaf is almost certainly in a CN1 region and needs to be excluded. See this post (and several others under the "sciclone" tag) for additional context https://www.biosta ...
written 9 weeks ago by Chris Miller20k

Latest awards to Chris Miller

Scholar 14 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Epic Question 5 weeks ago, created a question with more than 10,000 views. For Bioinformatics "Cheat Sheet"
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Scholar 4 months ago, created an answer that has been accepted. For A: How to aggregate multiple copy number variation profiles or select the best one
Scholar 4 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 4 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Student 4 months ago, asked a question with at least 3 up-votes. For Long-Term Hosting For Large Annotation Files?
Student 5 months ago, asked a question with at least 3 up-votes. For Importing A Large Number Of References From Text
Good Question 5 months ago, asked a question that was upvoted at least 5 times. For Importing A Large Number Of References From Text
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 5 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
Scholar 6 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Appreciated 6 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 8 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 10 months ago, created a question with more than 1,000 views. For Efficiently storing methylation data from BS-sequencing
Scholar 11 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1753 users visited in the last hour