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How To Set Up RStudio On A CentOS Cloud Server | DigitalOcean

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Check Linux release ls /etc/*release ## /etc/centos-release /etc/os-release /etc/redhat-release /etc/system-release cat /etc/redhat-release ## CentOS Linux release 7.3.1611 (Core) Install R # Install Extra Packages for Enterprise Linux repository configuration # R belongs to RHEL Extra Packages for Enterprise Linux (EPEL) # Extra Packages for Enterprise Linux (or EPEL) is a Fedora Special Interest Group that creates, maintains, and manages a high quality set of additional packages for Enterprise Linux sudo yum install -y epel-release sudo yum update -y sudo yum install -y R Install Rstudio server ## https://www.rstudio.com/products/rstudio/download-server/ wget https://download2.rstudio.org/rstudio-server-rhel-1.0.143-x86_64.rpm yum install --nogpgcheck rstudio-server-rhel-1.0.143-x86_64.rpm ## By default RStudio Server runs on port 8787 and accepts connections from all remote clients. After installation you should therefore be able to navigate a web browser to the fol...
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P and q values in RNA Seq

The q-value is an adjusted p-value, taking in to account the false discovery rate (FDR). Applying a FDR becomes necessary when we're measuring thousands of variables (e.g. gene expression levels) from a small sample set (e.g. a couple of individuals). A p-value of 0.05 implies that we are willing to accept that 5% of all tests will be false positives. An FDR-adjusted p-value (aka a q-value) of 0.05 implies that we are willing to accept that 5% of the tests found to be statistically significant (e.g. by p-value) will be false positives. Such an adjustment is necessary when we're making multiple tests on the same sample. See, for example, http://www.totallab.com/products/samespots/support/faq/pq-values.aspx. -HomeBrew What are p-values? The object of differential 2D expression analysis is to find those spots which show expression difference between groups, thereby signifying that they may be involved in some biological process of interest to the researcher. Due to chance, the...
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How to download reads from NCBI SRA database?

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1.  SRA explorer  This tool aims to make datasets within the Sequence Read Archive more accessible. SRA-Explorer allows you to collect SRA datasets and get a quick bash download script for either SRA files or now FastQ files! (courtesy of the ENA API) https://github.com/ewels/sra-explorer It doesn't have any extra functionality though, just finding URLs basically. If the ENA has a consistent FTL URL structure then it should be simple to extend it to work with direct FastQ downloads too though. 2.  enaBrowserTools A collection of scripts to assist in the retrieval of data from the ENA Browser 3.  pysradb Package for fetching metadata and downloading data from SRA Choudhary S. pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive [version 1; peer review: awaiting peer review]. F1000Research 2019, 8:532 ( https://doi.org/10.12688/f1000research.18676.1 ) 4. Downloading published fastq dat...
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