Recent Changes

Sunday, May 20

  1. page Molecular mechanisms of Alzheimer's disease edited ... Adrian asked if a specific twintron {twintron_adrian_2017-09-20.zip} is DE, which is not as …
    ...
    Adrian asked if a specific twintron {twintron_adrian_2017-09-20.zip} is DE, which is not as explained in Habil's email on 2017-09-20.
    Habil compared RNA-Seq vs. NanoString (See under 2018/04/25 in his lano).
    Habil's analysis on the human iPSC dataset did not identify any DE TE (see oncinfo/oncinfo/oncinfo/17).
    Small RNA Analysis
    Habil copied the fastq files from the dropbox folder in Zhao's email to the work directory on the Lonestar5 cluster. He created a symbolic link to them from his home directory. See ~/proj/alzheimer/data/Drosophila_2017-03-03/readme.txt.
    (view changes)
    6:56 pm
  2. 6:46 pm

Thursday, May 17

  1. page Molecular mechanisms of Alzheimer's disease edited ... Small RNA sequencing on the same above samples. Human RNA-Seq data from Mayo Clinic to test t…
    ...
    Small RNA sequencing on the same above samples.
    Human RNA-Seq data from Mayo Clinic to test these hypotheses, which Bess made based on Drosophila data. Specifically, the raw fastq files from MayoRNAseq dataset for NCI, PSP, AD, and PA (Synapse ID: syn5550404, cerebellum and temporal cortex).
    ...
    Neurology 2018 paper.paper (readme.txt).
    Collaborators
    Dr. Bess Frost from the Department of Structural and Cellular Biology at UT Health Science Center in San Antonio.
    (view changes)
    2:10 pm
  2. page Molecular mechanisms of Alzheimer's disease edited ... Small RNA sequencing on the same above samples. Human RNA-Seq data from Mayo Clinic to test t…
    ...
    Small RNA sequencing on the same above samples.
    Human RNA-Seq data from Mayo Clinic to test these hypotheses, which Bess made based on Drosophila data. Specifically, the raw fastq files from MayoRNAseq dataset for NCI, PSP, AD, and PA (Synapse ID: syn5550404, cerebellum and temporal cortex).
    Human RNA-seq data from iPSC-derived neurons from 3 patients with tauopathy, along with 3 CRISPR-corrected isogenic control samples. On 24 April 2018, Celeste Karch provided us with bam files of the data from their JAMA Neurology 2018 paper.
    Collaborators
    Dr. Bess Frost from the Department of Structural and Cellular Biology at UT Health Science Center in San Antonio.
    (view changes)
    2:05 pm

Monday, May 14

  1. page Hanie's lab notebook 2 edited ... inetgrator {inetgrator_2017-11-13.RData} General plan, microarray2symbol 2018-05-14 Worki…
    ...
    inetgrator {inetgrator_2017-11-13.RData}
    General plan, microarray2symbol
    2018-05-14
    Working on my proposal
    2018-04-03 : 2018-05-13
    Final exams and projects

    2018-04-29
    Applying for job
    (view changes)
    6:11 am

Wednesday, May 9

  1. page How to edited Install R package from source <span style="background-color: #eff0f1; color: #393318; f…

    Install R package from source
    <span style="background-color: #eff0f1; color: #393318; font-family: Consolas,Menlo,Monaco,&#39;Lucida Console&#39;,&#39;Liberation Mono&#39;,&#39;DejaVu Sans Mono&#39;,&#39;Bitstream Vera Sans Mono&#39;,&#39;Courier New&#39;,monospace,sans-serif; vertical-align: baseline;"><span style="font-family: Consolas,Menlo,Monaco,&#39;Lucida Console&#39;,&#39;Liberation Mono&#39;,&#39;DejaVu Sans Mono&#39;,&#39;Bitstream Vera Sans Mono&#39;,&#39;Courier New&#39;,monospace,sans-serif; vertical-align: baseline;"><span class="pln" style="color: #303336; font-family: inherit; vertical-align: baseline;">install.packages</span><span class="pun" style="color: #303336; font-family: inherit; vertical-align: baseline;">(</span><span class="pln" style="color: #303336; font-family: inherit; vertical-align: baseline;">path_to_file</span><span class="pun" style="color: #303336; font-family: inherit; vertical-align: baseline;">,</span><span class="pln" style="color: #303336; font-family: inherit; vertical-align: baseline;"> repos </span><span class="pun" style="color: #303336; font-family: inherit; vertical-align: baseline;">=</span><span class="lit" style="color: #7d2727; font-family: inherit; vertical-align: baseline;">NULL</span><span class="pun" style="color: #303336; font-family: inherit; vertical-align: baseline;">,</span><span class="pln" style="color: #303336; font-family: inherit; vertical-align: baseline;"> type</span><span class="pun" style="color: #303336; font-family: inherit; vertical-align: baseline;">=</span><span class="str" style="color: #7d2727; font-family: inherit; vertical-align: baseline;">"source"</span><span class="pun" style="color: #303336; font-family: inherit; vertical-align: baseline;">)</span></span></span>

    Read a gctx file?
    These are descriptions 1 and 2 for gctx format. The best way to read and convert gctx to gct is by GENE-E.
    (view changes)
    6:39 am

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