Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
Reputation:
16,320
Status:
Trusted
Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Scholar ID:
Google Scholar Page
Last seen:
9 hours ago
Joined:
7 years ago
Email:
l******@gmail.com

Bioinformatics software developer working at a pediatric hospital.

Posts by Jeremy Leipzig

<prev • 763 results • page 1 of 77 • next >
1
vote
1
answer
137
views
1
answers
Comment: C: GWAS & Logistic regression in R
... It's probably still ok to use GAPIT for this, you just have to round the responses to 0 or 1, assuming these responses are ordered in some meaningful way ...
written 14 days ago by Jeremy Leipzig16k
0
votes
1
answer
137
views
1
answers
Comment: C: GWAS & Logistic regression in R
... Is it continuous? ...
written 17 days ago by Jeremy Leipzig16k
1
vote
2
answers
795
views
2
answers
Comment: C: mitochondrial blacklists ATAC-Seq
... real NUMTs, assuming transposase binds to them, would map to the NUMT regions you list above. I don't know whether they would also align to chrM. Better to blacklist both chrM and the regions. ...
written 18 days ago by Jeremy Leipzig16k
1
vote
2
answers
795
views
2
answers
Comment: C: mitochondrial blacklists ATAC-Seq
... These homologous regions are called NUMTs ...
written 21 days ago by Jeremy Leipzig16k
0
votes
1
answer
137
views
1
answers
Answer: A: GWAS & Logistic regression in R
... A logistic regression is where your dependent, outcome variable is dichotomous or binary (aka logical). GAPIT is a mixed model linear regression, which means it tries to divide the regressors into fixed and random effects. This is super important in agriculture where most of all the GWAS signals en ...
written 25 days ago by Jeremy Leipzig16k
0
votes
0
answers
229
views
0
answers
Comment: C: hppRNA: a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of
... do you have something against github or even bitbucket? sourceforge is a ghost town ...
written 7 weeks ago by Jeremy Leipzig16k
2
votes
3
answers
673
views
3
answers
Comment: C: Example of how bioinformaticians can publish in Scientific Reports (by nature pu
... Right. Without source code this paper is certainly no example of reproducible research, even though being both *in silico* and based on public data, it was well suited to be an examplar. ...
written 11 weeks ago by Jeremy Leipzig16k
0
votes
3
answers
1.5k
views
3
answers
Answer: A: Bait/Target files for Picard HsMetrics (Exome Sequencing)
... cat nexterarapidcapture_exome_targetedregions_v1.2.bed | sed s/chr//g | sed s/M/MT/g > nexterarapidcapture_exome_targetedregions_v1.2.no_chr.MT.bed cat NexteraRapidCapture_Exome_Probes_v1.2.txt | grep CEX | sed -e 's/chrM/chrMT/g;s/chr//g;' | cut -f2,3,4 > NexteraRapidCapture_Exome_Pr ...
written 3 months ago by Jeremy Leipzig16k
0
votes
0
answers
2.4k
views
0
answers
Comment: C: Join us in building a bioinformatics resource: The Biostar Handbook
... I also feel there should be links to actual Biostars questions and tags at the bottom of each page. This handbook seems a bit divorced from Biostars as it stands. ...
written 4 months ago by Jeremy Leipzig16k
0
votes
1
answer
413
views
1
answers
Comment: C: How to analyze NGS data: An overview of nine different IT solutions
... it's probably wise to leave out examples - the whiners will come out in force claiming they have feature X or feature Y that makes the category meaningless ...
written 4 months ago by Jeremy Leipzig16k

Latest awards to Jeremy Leipzig

Popular Question 8 days ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Great Question 11 days ago, created a question with more than 5,000 views. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
Great Question 6 weeks ago, created a question with more than 5,000 views. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Is There A Convention For Representing Indels In Diploid Genome Sequences?
Popular Question 3 months ago, created a question with more than 1,000 views. For Is There A Convention For Representing Indels In Diploid Genome Sequences?
Student 3 months ago, asked a question with at least 3 up-votes. For Why Do Genbank And Refseq Have Different Coordinates For Mitochondrial Features?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Making bioinformatics help and tutorials open
Scholar 6 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Why Does Rna-Seq Read Count Fit Poisson Distribution?
Scholar 8 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Prophet 8 months ago, created a post with more than 20 followers. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
Popular Question 8 months ago, created a question with more than 1,000 views. For Why Isn'T Na12878 In All.2Of4Intersection.20100804.Genotypes.Vcf.Gz
Popular Question 9 months ago, created a question with more than 1,000 views. For Why Isn'T Na12878 In All.2Of4Intersection.20100804.Genotypes.Vcf.Gz
Scholar 9 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Popular Question 9 months ago, created a question with more than 1,000 views. For Why Isn'T Na12878 In All.2Of4Intersection.20100804.Genotypes.Vcf.Gz
Appreciated 9 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: No Reads Ever Map To First 3Million Bases Of Chromosomes In Mouse Genome! Why?
Student 10 months ago, asked a question with at least 3 up-votes. For What Are The Most Common Stupid Mistakes In Bioinformatics?
Popular Question 11 months ago, created a question with more than 1,000 views. For Why Isn'T Na12878 In All.2Of4Intersection.20100804.Genotypes.Vcf.Gz
Popular Question 11 months ago, created a question with more than 1,000 views. For Why Isn'T Na12878 In All.2Of4Intersection.20100804.Genotypes.Vcf.Gz
Student 11 months ago, asked a question with at least 3 up-votes. For Is There A Convention For Representing Indels In Diploid Genome Sequences?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 473 users visited in the last hour