User: krassowski.michal

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Posts by krassowski.michal

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Selecting the consensus/overlapped genes from the DE study
... I get the sentiment and agree that in an ideal scenario that would be the case, but I am not convinced that lowering the threshold will always have the same effect, especially if instead of taking overlap after thresholding one would choose to (wisely) combine p-values. What do you think? ...
written 6 months ago by krassowski.michal60
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Comment: C: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
... Please note that the limma manual recommends the use of EdgeR's TMM normalization rather than quantile normalization for RNASeq data (see [here](http://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf)). Also, both limma and DESeq2 have considerably changed since the ...
written 6 months ago by krassowski.michal60 • updated 12 days ago by RamRS25k
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Answer: A: Selecting the consensus/overlapped genes from the DE study
... Adding to the previous answer and comments: 1) this paper provides arguments in favour of the consensus approach: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190152. They benchmarked all three methods that you mention (and a couple more) and show that (given the datasets tha ...
written 6 months ago by krassowski.michal60
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Answer: A: How to calculate connectivity score for a compound in connectivity map O2?
... **Let's start with the calculation of the connectivity scores (*Si*):** For an instance *i* (i.e. a perturbagen in specific conditions - cell/dose/time), the final score *Si* depends on "preliminary" scores *si* of all other instances: For postively connected perturbagenes (instances with positive ...
written 9 months ago by krassowski.michal60
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Answer: A: How to calculate connectivity score for a compound in connectivity map O2?
... For anyone else interested: Here is a link to documentation of connectivity scores for the old CMap: https://portals.broadinstitute.org/cmap/help_topics_linkified.jsp (also nicely explained in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3868238/) And here the link to a description of scores in ne ...
written 12 months ago by krassowski.michal60
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Comment: C: TCGA barcode documentation? TCGA wiki?
... I found some useful hints on https://bioconductor.org/packages/3.7/bioc/vignettes/TCGAbiolinks/inst/doc/query.html ...
written 19 months ago by krassowski.michal60
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TCGA barcode documentation? TCGA wiki?
... Is there a publicly accessible website with detailed TCGA documentation, especially with TCGA barcode specification? A while ago there was: https://wiki.nci.nih.gov/display/TCGA/TCGA+Barcode (still indexed in Google, linked in a few Biostars responses and questions), but it now just shows an authent ...
barcode tcga written 19 months ago by krassowski.michal60
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Comment: C: dotplot with python
... You could also take a look at https://github.com/kn-bibs/dotplot ...
written 20 months ago by krassowski.michal60
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Answer: A: Is There Any Stand Alone Dot Plot Program?
... We wrote this small python script: https://pypi.python.org/pypi/dotplot/ which provides both CLI and GUI, although it is sequence based: ![GUI][1] [1]: https://raw.githubusercontent.com/kn-bibs/dotplot/master/gui.png ...
written 20 months ago by krassowski.michal60
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Comment: C: Retrieving Uniprot Protein Isoform Sequences Programmatically?
... Heads up: in 2018 this file contains only non-canonical splice variants (not all isoforms). Canonical isoforms are stored in [ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz](uniprot_sprot.fasta.gz) which is an order of magnitude bigger. ...
written 23 months ago by krassowski.michal60

Latest awards to krassowski.michal

Supporter 4 weeks ago, voted at least 25 times.
Popular Question 18 months ago, created a question with more than 1,000 views. For TCGA barcode documentation? TCGA wiki?

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