User: rf

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rf90
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Posts by rf

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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 13 days 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answers I got, or associated resources (e.g. [this][2]) either provide only information for the protocol, or provide [outdated links][3] or literature references.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 13 days 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 13 days ago by rf90 • updated 10 days 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 19 days 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 19 days 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 19 days 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 19 days ago by rf90 • updated 19 days ago by Kevin Blighe19k
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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 5 weeks ago by rf90
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Genome-wide CRISPR/Cas9 and gene expression?
... Is anyone aware of genome-wide CRISPR/Cas9 screens where gene expression is quantified? Meaning, after targeting a gene, what is the average gene expression change for all genes (microarray, RNAseq, etc.)? Thanks in advance ...
crispr gene expression cas9 microarray written 5 weeks ago by rf90
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Error in PIANO
... I am using PIANO to determine differentially expressed genes. My setup file looks like this: TYPE CELid1.CEL CONTROL CELid2.CEL CONTROL CELid3.CEL TREATMENT ... my annotation looks like this: SYMBOL chromoso ...
R chip-seq piano written 6 months ago by rf90

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Popular Question 5 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
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Popular Question 8 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 10 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 15 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 15 months ago, created a question with more than 1,000 views. For BioPerl retrieves joined sequence incorrectly
Popular Question 19 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 2.8 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 3.3 years ago, created an answer that has been accepted. For A: How to skip a genebank file that has no dna sequence?
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