Moderator: karl.stamm

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karl.stamm3.6k
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Posts by karl.stamm

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Answer: A: DESeq2 Error: package or namespace load failed for 'DESeq2'
... The error message says you're missing libopenblasp-r0.3.7.dylib. Installing openblas could fix it, and there's several suggestions to reinstall R itself to gather the assumed dependencies. https://stackoverflow.com/questions/50634727/dyld-library-not-loaded-usr-local-opt-openblas-lib-libopenblasp-r0 ...
written 5 weeks ago by karl.stamm3.6k
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Comment: C: Validation microarray data by R, "Need BasicTutorials"
... it's not clear what you're trying to do. Validate can mean many things. ...
written 6 weeks ago by karl.stamm3.6k
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Answer: A: How to extract sequences from multi fasta file, which contains specific primers?
... try "grep" http://linuxcommand.org/lc3_man_pages/grep1.html or https://ss64.com/osx/grep.html very important command line program to know. grep simply searches the file for you. You asked "How can i do it with awk or sed or grep" and that's a homework question. Look up what each tool doe ...
written 7 weeks ago by karl.stamm3.6k
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Answer: A: Editing source scripts in a container
... That's normal behavior for docker, no changes are saved by design. You can put the modifications into the scripts that run on startup, that way the changes are executed in each container anew. Using a script to modify the samtools sort commands may be tricky, so perhaps having it download a comple ...
written 11 weeks ago by karl.stamm3.6k
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Comment: C: how to download a list of snps with all details for a specific gene from Ensembl
... One question at a time! The essence of computer programming is to break down your question into steps that can be solved. You want to download SNP data, does it have to be from Ensembl? If that's difficult, consult their documentation. Or is Biomart really necessary? maybe they have tutorials at th ...
written 3 months ago by karl.stamm3.6k
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Comment: C: Fisher strand (FS) 0?
... p-values are not effect sizes. Anything p>0.2 is equivalent to saying 'no evidence' you shouldn't judge the difference between a p=0.5 and a p=0.9 to mean anything at all. They tend to get conflated with strength of association, because in introductory statistics they may appear to be correlated, ...
written 4 months ago by karl.stamm3.6k
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Comment: C: Fisher strand (FS) 0?
... This one https://gatkforums.broadinstitute.org/gatk/discussion/6724/question-for-fisherstrand seems to say that high FS indicates strand bias, and possibly false positives from low coverage regions. Makes sense that a position with "25,19:17,12" has really 0 apparent strand bias. ...
written 4 months ago by karl.stamm3.6k
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Comment: C: Fisher strand (FS) 0?
... What tool generated this data? Including the command line can be helpful too. From what I can interpret of the data you posted originally, it looks like quite a normal HET, with basically balanced reads. What did you expect of the FS field? ...
written 4 months ago by karl.stamm3.6k
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Comment: C: Should I Run Clustering on PCA or t-SNE Components?
... and dont forget to look at PCA dimensions 3&4, there's so much beyond dimensions 1&2. ...
written 5 months ago by karl.stamm3.6k
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Comment: C: Should I Run Clustering on PCA or t-SNE Components?
... Plain PCA on the whole dataset gives the broadest picture. it is vulnerable to scaling problems: if there are two major clusters very distinct, like dead cell / alive cell, you wont be able to see nuanced differences in alive cell type A vs B. That's where a rescaler like tSNE or UMAP can be helpfu ...
written 5 months ago by karl.stamm3.6k

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Scholar 6 months ago, created an answer that has been accepted. For A: multithreading in psiblast
Scholar 6 months ago, created an answer that has been accepted. For A: multithreading in psiblast
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Can I run VEP on a VCF twice?
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
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Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Scholar 3.3 years ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Commentator 3.8 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Commentator 3.8 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Appreciated 3.9 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 4.0 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Scholar 4.1 years ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Appreciated 4.1 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Good Answer 4.1 years ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
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