User: krassowski.michal

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Posts by krassowski.michal

<prev • 12 results • page 1 of 2 • next >
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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 5 weeks ago by krassowski.michal40
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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 3 months ago by krassowski.michal40
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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 10 months ago by krassowski.michal40
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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 10 months ago by krassowski.michal40
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Comment: C: dotplot with python
... You could also take a look at https://github.com/kn-bibs/dotplot ...
written 11 months ago by krassowski.michal40
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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 11 months ago by krassowski.michal40
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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 14 months ago by krassowski.michal40
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What is the licence of NCBI RefSeq database?
... This might not be a usual question here, but I struggle to find terms & conditions of use of NCBI RefSeq database and licence of the database. I think I managed to find it somewhere a long time ago but cannot recollect where it was. I checked https://www.ncbi.nlm.nih.gov/books/NBK21091/ (it only ...
ncbi refseq written 17 months ago by krassowski.michal40 • updated 13 months ago by tdmurphy160
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Comment: C: Bulk Download Of Ncbi Gene "Summary" Field
... That is strange, indeed. For me it's working and retrieves gzipped summary with weight about 5.4MB. I tested it right now on Ubuntu 17.04 with GNU Wget 1.18 and GNU sed 4.4. Looking at your logs I found `oupu` instead of `output`, `posiion` instead of `position`. I guess either your bash or your ve ...
written 19 months ago by krassowski.michal40
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Comment: C: Bulk Download Of Ncbi Gene "Summary" Field
... The output looks good. Where is the problem? Are you able to open summary.tsv.gz? ...
written 19 months ago by krassowski.michal40

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Popular Question 9 months ago, created a question with more than 1,000 views. For TCGA barcode documentation? TCGA wiki?

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