User: e.rempel

gravatar for e.rempel
e.rempel770
Reputation:
770
Status:
Trusted
Location:
Germany, Heidelberg, COS
Last seen:
1 month ago
Joined:
4 years, 5 months ago
Email:
e*******@dkfz-heidelberg.de

Statistician/bioinformatician.

Posts by e.rempel

<prev • 90 results • page 1 of 9 • next >
0
votes
0
answers
142
views
0
answers
Understanding the output of pileup2snp
... Hi, I have a question regarding the output of the tool *varscan pileup2snp*. The input is the pileup file generated by *samtools mpileup* without reference. One particular line from the input is 1 16259813 N 80 G$g$aaGAGAaggaAGGaaGaGAgaAGaAgAAGGaAAAAAGAAaaGAaGgGgAGaGAGAgGggGAAAAgAAGgggAGGGAA^] ...
variant samtools snp varscan written 7 weeks ago by e.rempel770
0
votes
1
answer
457
views
1
answer
bcl2fastq creates only Undetermined fastq
... Hi everyone, I have a question regarding the usage of **bcl2fastq** for an Agilent panel. The manufacture suggests [in this guide][1] to use the parameter "---use-bases-mask" with the specification Y\*,I8,Y10,Y\*. Bcl2fastq throws in this case the error: UseBasesMask formatting e ...
software error sequencing written 5 months ago by e.rempel770 • updated 5 months ago by genomax71k
0
votes
2
answers
5.4k
views
2
answers
Comment: C: aligning with STAR
... After depreciation of homebrew/science you have to use brew tab brewsci/science brew install rna-star ...
written 16 months ago by e.rempel770
1
vote
1
answer
650
views
1
answers
Comment: C: Clustering and extracting gene IDs with same expression profiles
... Hi, in the example from [Bioconductor][1] the object after **cutree** execution contains the genes with the cluster identifier (a number from one to n - an integer you have chosen for cutree). [1]: https://support.bioconductor.org/p/93424/ ...
written 18 months ago by e.rempel770
1
vote
2
answers
981
views
2
answers
Answer: A: On the significance of the overlap between lists of genes
... Hi, as you said, the p-value of Fisher's exact test is highly significant. The reason for this, as you have also said, is the size of gene's universe. I have seen some people making thoughts about the universe: can any random gene from these 17611 genes be selected in any of your lists? Sometimes ...
written 18 months ago by e.rempel770
0
votes
2
answers
646
views
2
answers
Comment: C: Submission of RNA-seq data in NCBI Sequence Read Archive (SRA)
... Please, consider upvoting ("thumbs up") or accepting the answer, if it clarifies the issue for you. ...
written 19 months ago by e.rempel770
0
votes
1
answer
630
views
1
answers
Comment: C: Getting MDSplot from Cufflinks data [cummeRbund]
... I am not a huge expert on cummeRbund, but it looks like you first extract the genes from `cuff` object, then you use them to create MDS-plot. Usually, the input for MDS (or PCA) is some rectangular data, e.g. genes in rows, samples in columns. For me it looks like you are using just "genes". Am I ri ...
written 19 months ago by e.rempel770
2
votes
1
answer
4.0k
views
1
answers
Comment: C: scatter plot in ggplot2 two colour for two different condition
... Just hook your boss up on [biostars][1] ;) [1]: http://biostars.org ...
written 19 months ago by e.rempel770
2
votes
1
answer
4.0k
views
1
answers
Comment: C: scatter plot in ggplot2 two colour for two different condition
... So, what should colour represent? I honestly don't get it. ...
written 19 months ago by e.rempel770
2
votes
1
answer
431
views
1
answers
Answer: A: try command in R
... Hi, quick Google search redirected me to the [book][1] of Hadley Wickham. Here he suggests: > To pass larger blocks of code to try(), wrap them in {}: try({ a <- 1 b <- "x" a + b }) HTH [1]: http://adv-r.had.co.nz/ ...
written 19 months ago by e.rempel770

Latest awards to e.rempel

Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: GO analysis using topGO Arabidopsis
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with topGO: GO term enrichment analysis
Appreciated 11 months ago, created a post with more than 5 votes. For A: GO analysis using topGO Arabidopsis
Scholar 11 months ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis
Appreciated 18 months ago, created a post with more than 5 votes. For A: GO analysis using topGO Arabidopsis
Scholar 22 months ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Appreciated 2.0 years ago, created a post with more than 5 votes. For A: GO analysis using topGO Arabidopsis
Scholar 2.0 years ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Scholar 2.0 years ago, created an answer that has been accepted. For A: Heatmap.2 giving specific color to a value and start gradient after
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis
Supporter 2.1 years ago, voted at least 25 times.
Scholar 2.1 years ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis
Scholar 2.1 years ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Scholar 2.1 years ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: GO analysis using topGO Arabidopsis
Scholar 2.4 years ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 583 users visited in the last hour