User: Michael Schubert

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Cambridge, UK
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Posts by Michael Schubert

<prev • 531 results • page 1 of 54 • next >
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Comment: C: Differences between FPKM and FPKM-UQ files in gene expression analysis
... To add the actual answer: "The upper quartile FPKM (FPKM-UQ) is a modified FPKM calculation in which the total protein-coding read count is replaced by the 75th percentile read count value for the sample." ...
written 21 months ago by Michael Schubert6.9k
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Answer: A: How to download a whole ICGC release of processed data?
... I wrote a script that seems to do it reasonably well: https://gist.github.com/mschubert/cf364c1e9ce7f4a5e91be1da6f28c3a2 ...
written 2.8 years ago by Michael Schubert6.9k
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How to download a whole ICGC release of processed data?
... The ICGC moved from FTP access to their new data portal where they provide releases of the *processed* data: https://dcc.icgc.org/releases/release_23 How can I download the whole release? A machine readable collection of all links is not available, `wget` doesn't do it because it's Java-script ba ...
icgc download written 2.8 years ago by Michael Schubert6.9k
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Comment: C: Connectivity Map file names
... Note that this is not the latest version which can be reached at http://www.lincscloud.org/ or https://clue.io/ ...
written 3.8 years ago by Michael Schubert6.9k
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Comment: C: R package for GSEA
... piano (BioConductor) is another; there are also some set statistics implemented in limma (see https://www.bioconductor.org/packages/3.3/bioc/manuals/limma/man/limma.pdf, romer, roast, camera) ...
written 4.0 years ago by Michael Schubert6.9k
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Comment: C: How to judge severity of variants in genes
... Unless I understand something wrong, the "severity" you are looking for is functional impact. This is exactly what the tools above do. I am not aware of any systematic bias if short indels closer to the stop codon as opposed to other segments of the gene. ...
written 4.0 years ago by Michael Schubert6.9k
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Answer: A: How to judge severity of variants in genes
... There are plenty of tools out there that try to assess the impact of different mutations (including indels) in proteins. Have a look at: http://www.ensembl.org/info/docs/tools/vep/index.html > The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural varia ...
written 4.0 years ago by Michael Schubert6.9k
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Comment: C: Installation of the MuSiC suite on unsupported Linux distributions
... "`which cpanm`" is not required, "cpanm" is enough (bash will resolve this automatically) ...
written 4.2 years ago by Michael Schubert6.9k
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Answer: A: For R workshop, need bio equivalent of 'diamonds' or 'nycflights13' data.
... How about some data from the TCGA? They have text tables on http://gdac.broadinstitute.org/, e.g. breast cancer clinical data. Note: be sure to check the TCGA guidelines for what you can use the data ...
written 4.8 years ago by Michael Schubert6.9k
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Comment: C: What Are The Main Advantages Of Ngs Over Arrays In Transcriptomics?
... higher dynamic range and sequence information ...
written 5.8 years ago by Michael Schubert6.9k

Latest awards to Michael Schubert

Popular Question 2.3 years ago, created a question with more than 1,000 views. For Finding Class-Discriminant Genes In A Microarray Experiment
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Ncbi Legacy Blast Usage With Tblastn/Pssm
Appreciated 2.3 years ago, created a post with more than 5 votes. For C: Is The Biostar Fading? (Updated For 2014)
Appreciated 2.3 years ago, created a post with more than 5 votes. For C: C Programing In Bioinformatics
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Best Genome Browser To Look At Structural Variation Calls
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Extract Sequence From Record And Feature Location
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Best Genome Browser To Look At Structural Variation Calls
Scholar 2.8 years ago, created an answer that has been accepted. For A: Machine Learning And Chip-Seq
Commentator 3.6 years ago, created a comment with at least 3 up-votes. For C: Getting Experience In Bioinformatics
Appreciated 3.6 years ago, created a post with more than 5 votes. For C: C Programing In Bioinformatics
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Best Genome Browser To Look At Structural Variation Calls
Good Question 3.6 years ago, asked a question that was upvoted at least 5 times. For Finding Class-Discriminant Genes In A Microarray Experiment
Great Question 3.6 years ago, created a question with more than 5,000 views. For How To Create A Pssm From Fasta Homologues With Ncbi Blast+ 2.2.23
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Use Conservation Or Evolutionary Rate To Infer Functional Relevance Of Aminoacid
Appreciated 3.7 years ago, created a post with more than 5 votes. For C: C Programing In Bioinformatics
Scholar 3.7 years ago, created an answer that has been accepted. For A: Machine Learning And Chip-Seq
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Opening Biogrid Files In Cytoscape
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How To Scale A Pssm For Ncbi Blast
Appreciated 3.9 years ago, created a post with more than 5 votes. For C: C Programing In Bioinformatics
Appreciated 4.0 years ago, created a post with more than 5 votes. For C: C Programing In Bioinformatics
Appreciated 4.2 years ago, created a post with more than 5 votes. For C: C Programing In Bioinformatics
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Opening Biogrid Files In Cytoscape
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Opening Biogrid Files In Cytoscape
Good Answer 4.3 years ago, created an answer that was upvoted at least 5 times. For A: Machine Learning And Chip-Seq
Appreciated 4.3 years ago, created a post with more than 5 votes. For Searching For Specific Protein Domains In Rna-Seq

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