User: rf

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rf90
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Posts by rf

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Comment: C: Genome-wide CRISPR/Cas9 and gene expression?
... For many reasons, it would be great to have this sort of gene expression response to genome-wide screens. E.g. assessing pathway adaptation or response to knockout, finding potential therapeutic targets, determining gene essentiality. Though the last point may be somewhat addressed using existing d ...
written 11 weeks ago by rf90
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Comment: C: Genome-wide CRISPR/Cas9 and gene expression?
... Absolutely, that is exactly what I wanted to see! :) ...
written 11 weeks ago by rf90
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Comment: C: Where to find CCLE metadata?
... I have contacted them about 3-4 weeks ago and am still waiting for their reply. Hopefully, we'll get a comment here since the account requirement is free ...
written 3 months ago by rf90
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Comment: C: Where to find CCLE metadata?
... Note that I had previously asked about the RNASeq protocol in CCLE ([see here][1]). However, the answers I got, or associated resources (e.g. [this][2]) either provide only information for the protocol, or provide [outdated links][3] or literature references. [1]: https://www.biostars.org/p/3137 ...
written 3 months ago by rf90
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Where to find CCLE metadata?
... I'm looking for information on the cell lines from CCLE. For instance, you can find 2012 information in here: [https://portals.broadinstitute.org/ccle/data][1] under "Cell Line Annotations (1)". Anyone knows where I can find the most recent version? Thanks in advance [1]: https://portals.broa ...
ccle rna-seq written 3 months ago by rf90 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: RNA-seq data from CCLE - where are the details?
... This is great, thanks so much! ...
written 3 months ago by rf90
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Comment: C: RNA-seq data from CCLE - where are the details?
... @i,sudbery thanks. Do you have the reference for the publication? ...
written 3 months ago by rf90
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Comment: C: RNA-seq data from CCLE - where are the details?
... Ola'! Many thanks for your response! Unfortunately, they do not mention the procedures for RNAseq processing, and perhaps they have changed them in the last 6 years? ...
written 3 months ago by rf90
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RNA-seq data from CCLE - where are the details?
... I'd like to use the RNA-seq data from CCLE found at [https://portals.broadinstitute.org/ccle/data][1]. Where may I find more information about the methods that were considered to process the data? Thanks in advance rf [1]: https://portals.broadinstitute.org/ccle/data ...
gene ccle rna-seq written 3 months ago by rf90 • updated 3 months ago by Kevin Blighe26k
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Comment: C: Genome-wide CRISPR/Cas9 and gene expression?
... Yeah... An important challenge is that for whole-genome targeting, even if you consider only the 20k protein-coding genes, even microarray analyses become expensive. Especially if you consider any replicates ...
written 4 months ago by rf90

Latest awards to rf

Popular Question 8 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: theory behind the differential expression
Popular Question 11 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 13 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 18 months ago, created a question with more than 1,000 views. For How to debug (and solve) Bioperl problems when a gbk file doesn't have the genome?
Popular Question 18 months ago, created a question with more than 1,000 views. For BioPerl retrieves joined sequence incorrectly
Popular Question 22 months ago, created a question with more than 1,000 views. For How to debug (and solve) Bioperl problems when a gbk file doesn't have the genome?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to retrieve gene sequences and their products from NCBI's FTP?
Scholar 3.5 years ago, created an answer that has been accepted. For A: How to skip a genebank file that has no dna sequence?
Supporter 3.8 years ago, voted at least 25 times.

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