User: rf

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rf100
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Posts by rf

<prev • 75 results • page 1 of 8 • next >
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Homer not finding any genomes?
... I am creating the tagdirectories using Homer but can't get it to find the installed genome. I am running > makeTagDirectory $tagdirname/$filename\_tagDir -format HiCsummary $filename\_Summary.txt -illuminaPE -removePEbg -restrictionSite GATC -genome mm10 -tbp 1 But get the error !!! Coul ...
homer chip-seq hic written 4 days ago by rf100
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Answer: A: Enrichr : how to provide background as gene symbols or int ?
... ***1. Is it possible to provide this background as human gene symbols? If so, how?*** Writing `background=hsapiens_gene_ensembl` allows to use gene symbols, not only ensembl ids. ***2. May I provide the background myself? I want to have a smaller set of genes as background.*** The latest comm ...
written 4 weeks ago by rf100
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Enrichr : how to provide background as gene symbols or int ?
... I am using enrichr to perform some enrichment analyses. In their documentation they say that you can indicate the background list, or simply a number of genes for the background: > background (int) – BioMart dataset name for retrieving background gene > information. This argument only works w ...
gene microarray rna-seq gsea written 4 weeks ago by rf100
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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 9 months ago by rf100
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Comment: C: Genome-wide CRISPR/Cas9 and gene expression?
... Absolutely, that is exactly what I wanted to see! :) ...
written 9 months ago by rf100
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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 10 months ago by rf100
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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 10 months ago by rf100
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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 10 months ago by rf100 • updated 10 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 10 months ago by rf100
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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 10 months ago by rf100

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Popular Question 28 days ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 12 weeks 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?
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Popular Question 6 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 Any tools for predicting protein solvent exposure/accessibility?
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: theory behind the differential expression
Popular Question 18 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 20 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 2.1 years 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 2.1 years ago, created a question with more than 1,000 views. For BioPerl retrieves joined sequence incorrectly
Popular Question 2.4 years 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 3.6 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 4.1 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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